3H9M | pdb_00003h9m

Crystal structure of para-aminobenzoate synthetase, component I from Cytophaga hutchinsonii

PDB DOI: https://doi.org/10.2210/pdb3H9M/pdb

Classification: LYASE
Organism(s): Cytophaga hutchinsonii ATCC 33406
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-04-30 Released: 2009-06-30
Deposition Author(s): Sampathkumar, P., Atwell, S., Wasserman, S., Do, J., Bain, K., Rutter, M., Gheyi, T., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.192 (Depositor), 0.206 (DCC)
R-Value Work:
0.173 (Depositor), 0.186 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of para-aminobenzoate synthetase, component I from Cytophaga hutchinsonii

Sampathkumar, P., Atwell, S., Wasserman, S., Do, J., Bain, K., Rutter, M., Gheyi, T., Sauder, J.M., Burley, S.K.

To be published.

Macromolecule Content

Total Structure Weight: 49.78 kDa
Atom Count: 3,562
Modeled Residue Count: 399
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
p-aminobenzoate synthetase, component I	A	436	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0 Gene Names: CHU_1808, pabB, YP_678417.1 EC: 4.1.3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTU Query on DTU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-ZXZARUISSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-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: 1.57 Å
R-Value Free: 0.192 (Depositor), 0.206 (DCC)
R-Value Work: 0.173 (Depositor), 0.186 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.006	α = 90
b = 159.497	β = 90
c = 115.542	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
HKL2Map	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2018-11-21
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-04-03
Changes: Data collection, Database references, Refinement description
Version 1.6: 2024-11-20
Changes: Structure summary