3DIP

Crystal structure of an enolase protein from the environmental genome shotgun sequencing of the Sargasso Sea

PDB DOI: https://doi.org/10.2210/pdb3DIP/pdb

Classification: LYASE
Organism(s): unidentified
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-20 Released: 2008-07-29
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Zhang, F., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.275
R-Value Work: 0.215
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of an enolase protein from the environmental genome shotgun sequencing of the Sargasso Sea

Bonanno, J.B., Freeman, J., Bain, K.T., Zhang, F., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 88.74 kDa
Atom Count: 5,817
Modelled Residue Count: 738
Deposited Residue Count: 820
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
enolase	A, B	410	unidentified	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B]	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SIC Query on SIC	A, B	L-PEPTIDE LINKING	C₇ H₁₀ N₂ O₄ S		ASP, CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.275
R-Value Work: 0.215
R-Value Observed: 0.218
Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 282.292	α = 90
b = 282.292	β = 90
c = 282.292	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-11-14
Changes: Data collection, Database references, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references

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3DIP

Crystal structure of an enolase protein from the environmental genome shotgun sequencing of the Sargasso Sea

Crystal structure of an enolase protein from the environmental genome shotgun sequencing of the Sargasso Sea

Entity ID: 1

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)