3CPX | pdb_00003cpx

Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution

PDB DOI: https://doi.org/10.2210/pdb3CPX/pdb

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

Deposited: 2008-04-01 Released: 2008-04-29
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.223 (Depositor), 0.279 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative M42 glutamyl aminopeptidase (YP_676701.1) from Cytophaga hutchinsonii ATCC 33406 at 2.39 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 112.14 kDa
Atom Count: 7,728
Modeled Residue Count: 929
Deposited Residue Count: 963
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase, M42 family	A, B, C	321	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0 Gene Names: YP_676701.1, frvX, CHU_0067

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain S [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain S [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] L [auth B] M [auth B] P [auth C] D [auth A], E [auth A], L [auth B], M [auth B], P [auth C], Q [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.223 (Depositor), 0.279 (DCC)
R-Value Work: 0.187 (Depositor)
R-Value Observed: 0.189 (Depositor)

Diffraction Data:

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.84	α = 90
b = 83.84	β = 90
c = 682.31	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SOLVE	phasing
PHENIX	phasing
SHELXD	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-04-29

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-04-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, Structure summary