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- PDB-2ger: Crystal Structure and Oxidative Mechanism of Human Pyrroline-5-ca... -

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Basic information

Entry
Database: PDB / ID: 2ger
TitleCrystal Structure and Oxidative Mechanism of Human Pyrroline-5-carboxylate Reductase
ComponentsPyrroline-5-carboxylate reductase 1
KeywordsOXIDOREDUCTASE / Oxidative Mechanism of Human Pyrroline-5-carboxylate
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / Glutamate and glutamine metabolism / proline biosynthetic process / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of mitochondrial membrane potential / cellular response to oxidative stress / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
ProC C-terminal domain-like / ProC C-terminal domain-like fold / : / Delta 1-pyrroline-5-carboxylate reductase signature. / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily ...ProC C-terminal domain-like / ProC C-terminal domain-like fold / : / Delta 1-pyrroline-5-carboxylate reductase signature. / Pyrroline-5-carboxylate reductase / Pyrroline-5-carboxylate reductase, dimerisation domain / Pyrroline-5-carboxylate reductase dimerisation / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsMeng, Z. / Lou, Z. / Liu, Z. / Rao, Z.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of human pyrroline-5-carboxylate reductase
Authors: Meng, Z. / Lou, Z. / Liu, Z. / Li, M. / Zhao, X. / Bartlam, M. / Rao, Z.
History
DepositionMar 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrroline-5-carboxylate reductase 1
B: Pyrroline-5-carboxylate reductase 1
C: Pyrroline-5-carboxylate reductase 1
D: Pyrroline-5-carboxylate reductase 1
E: Pyrroline-5-carboxylate reductase 1


Theoretical massNumber of molelcules
Total (without water)168,1545
Polymers168,1545
Non-polymers00
Water10,755597
1
A: Pyrroline-5-carboxylate reductase 1


Theoretical massNumber of molelcules
Total (without water)33,6311
Polymers33,6311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Pyrroline-5-carboxylate reductase 1


Theoretical massNumber of molelcules
Total (without water)33,6311
Polymers33,6311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Pyrroline-5-carboxylate reductase 1


Theoretical massNumber of molelcules
Total (without water)33,6311
Polymers33,6311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Pyrroline-5-carboxylate reductase 1


Theoretical massNumber of molelcules
Total (without water)33,6311
Polymers33,6311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: Pyrroline-5-carboxylate reductase 1


Theoretical massNumber of molelcules
Total (without water)33,6311
Polymers33,6311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
D: Pyrroline-5-carboxylate reductase 1

E: Pyrroline-5-carboxylate reductase 1


Theoretical massNumber of molelcules
Total (without water)67,2622
Polymers67,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8670 Å2
ΔGint-97 kcal/mol
Surface area22520 Å2
MethodPISA
7
A: Pyrroline-5-carboxylate reductase 1

C: Pyrroline-5-carboxylate reductase 1


Theoretical massNumber of molelcules
Total (without water)67,2622
Polymers67,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8640 Å2
ΔGint-93 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.607, 123.805, 120.790
Angle α, β, γ (deg.)90.00, 121.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Pyrroline-5-carboxylate reductase 1 / P5CR 1 / P5C reductase 1


Mass: 33630.891 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P32322, pyrroline-5-carboxylate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8-1M sodium acetate, 30-40mM imidazole, 50-60mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 10, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 239961 / Num. obs: 239396 / % possible obs: 99 % / Observed criterion σ(F): 0
Reflection shellResolution: 3.1→3.2 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data reduction
SHELXmodel building
CNS1refinement
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.261 2326 random
Rwork0.233 --
all0.24 47236 -
obs0.235 46587 -
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10171 0 0 597 10768
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.007
X-RAY DIFFRACTIONc_bond_d1.466

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