3DUV

Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy-manno-octulosonate in the-configuration

PDB DOI: https://doi.org/10.2210/pdb3DUV/pdb

Classification: TRANSFERASE
Organism(s): Haemophilus influenzae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-18 Released: 2008-12-09
Deposition Author(s): Yoon, H.J., Ku, M.J., Mikami, B., Suh, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236
R-Value Work: 0.170
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 59.99 kDa
Atom Count: 4,080
Modelled Residue Count: 492
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-deoxy-manno-octulosonate cytidylyltransferase	A, B	262	Haemophilus influenzae	Mutation(s): 0 Gene Names: kdsB EC: 2.7.7.38
UniProt
Find proteins for P44490 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44490 Go to UniProtKB: P44490
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P44490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4C Query on P4C Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL C₁₄ H₂₈ O₈ CTLLATPOKUEFSQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
KDO Query on KDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid C₈ H₁₄ O₈ NNLZBVFSCVTSLA-HXUQBWEZSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.236
R-Value Work: 0.170
R-Value Observed: 0.177
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.418	α = 90
b = 82.609	β = 90
c = 115.712	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-12-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary

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3DUV

Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy-manno-octulosonate in the-configuration

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)