4JNN

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with benzamidine

PDB DOI: https://doi.org/10.2210/pdb4JNN/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Saccharomonospora viridis DSM 43017
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-03-15 Released: 2013-04-10
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.266
R-Value Work: 0.198
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with benzamidine

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 23 kDa
Atom Count: 1,595
Modelled Residue Count: 191
Deposited Residue Count: 194
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A	194	Saccharomonospora viridis DSM 43017	Mutation(s): 0 Gene Names: Svir_16270
UniProt
Find proteins for C7MT25 (Saccharomonospora viridis (strain ATCC 15386 / DSM 43017 / JCM 3036 / NBRC 12207 / P101)) Explore C7MT25 Go to UniProtKB: C7MT25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7MT25
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.266
R-Value Work: 0.198
R-Value Observed: 0.202
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.18430/M34JNN

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.791	α = 90
b = 109.952	β = 90
c = 76.875	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection

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Help and Resources

4JNN

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with benzamidine

Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with benzamidine

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)