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- PDB-2gr9: Crystal structure of P5CR complexed with NADH -

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Basic information

Entry
Database: PDB / ID: 2gr9
TitleCrystal structure of P5CR complexed with NADH
ComponentsPyrroline-5-carboxylate reductase 1
KeywordsOXIDOREDUCTASE / crystal strucutre / Human Pyrroline-5-carboxylate Reductase / nadh
Function / homology
Function and homology information


pyrroline-5-carboxylate reductase / pyrroline-5-carboxylate reductase activity / proline biosynthetic process / L-proline biosynthetic process / Glutamate and glutamine metabolism / 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 / NAD(P)-binding Rossmann-like Domain ...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
GLUTAMIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Pyrroline-5-carboxylate reductase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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
DepositionApr 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 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 6, 2013Group: Non-polymer description
Revision 1.4Sep 9, 2020Group: Database references / Derived calculations / Category: struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id ..._struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,80115
Polymers145,7385
Non-polymers4,06310
Water11,584643
1
A: Pyrroline-5-carboxylate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9603
Polymers29,1481
Non-polymers8132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Pyrroline-5-carboxylate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9603
Polymers29,1481
Non-polymers8132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Pyrroline-5-carboxylate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9603
Polymers29,1481
Non-polymers8132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Pyrroline-5-carboxylate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9603
Polymers29,1481
Non-polymers8132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: Pyrroline-5-carboxylate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9603
Polymers29,1481
Non-polymers8132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
D: Pyrroline-5-carboxylate reductase 1
hetero molecules

E: Pyrroline-5-carboxylate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9206
Polymers58,2952
Non-polymers1,6254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10930 Å2
ΔGint-109 kcal/mol
Surface area22090 Å2
MethodPISA
7
A: Pyrroline-5-carboxylate reductase 1
hetero molecules

C: Pyrroline-5-carboxylate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9206
Polymers58,2952
Non-polymers1,6254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10880 Å2
ΔGint-106 kcal/mol
Surface area22370 Å2
MethodPISA
8
B: Pyrroline-5-carboxylate reductase 1
hetero molecules

B: Pyrroline-5-carboxylate reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9206
Polymers58,2952
Non-polymers1,6254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10690 Å2
ΔGint-105 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.182, 122.642, 120.708
Angle α, β, γ (deg.)90.00, 122.03, 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: 29147.648 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: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O

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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: 4.48 Å3/Da / Density % sol: 72.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8-1M sodium acetate, 30-40mM imidazole (pH 6.5), 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 17, 2005
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 159528 / Num. obs: 158126 / % possible obs: 99 % / Observed criterion σ(F): 0
Reflection shellResolution: 3.1→3.2 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CrystalCleardata collection
HKL-2000data reduction
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GER

2ger


Resolution: 3.1→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 3031 random
Rwork0.241 --
all0.246 63370 -
obs0.243 59968 -
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10169 0 265 643 11077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.939
X-RAY DIFFRACTIONc_bond_d0.016

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