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- PDB-1vlu: Crystal structure of Gamma-glutamyl phosphate reductase (yor323c)... -

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Basic information

Entry
Database: PDB / ID: 1vlu
TitleCrystal structure of Gamma-glutamyl phosphate reductase (yor323c) from Saccharomyces cerevisiae at 2.40 A resolution
ComponentsGamma-glutamyl phosphate reductase
KeywordsOXIDOREDUCTASE / yor323c / GAMMA-GLUTAMYL PHOSPHATE REDUCTASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


Glutamate and glutamine metabolism / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / proline biosynthetic process / L-proline biosynthetic process / NADP binding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Glutamate-5-semialdehyde dehydrogenase / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Glutamate-5-semialdehyde dehydrogenase / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Gamma-glutamyl phosphate reductase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.29 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Gamma-glutamyl phosphate reductase (yor323c) from Saccharomyces cerevisiae at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-glutamyl phosphate reductase
B: Gamma-glutamyl phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2935
Polymers103,1862
Non-polymers1063
Water2,234124
1
A: Gamma-glutamyl phosphate reductase
hetero molecules

A: Gamma-glutamyl phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3998
Polymers103,1862
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
B: Gamma-glutamyl phosphate reductase

B: Gamma-glutamyl phosphate reductase


Theoretical massNumber of molelcules
Total (without water)103,1862
Polymers103,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)123.041, 191.081, 125.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: HIS / End label comp-ID: TYR / Refine code: 5 / Auth seq-ID: 0 - 435 / Label seq-ID: 12 - 447

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Gamma-glutamyl phosphate reductase / GPR / Glutamate-5-semialdehyde dehydrogenase / Glutamyl-gamma-semialdehyde dehydrogenase / GSA dehydrogenase


Mass: 51593.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRO2, YOR323C / Production host: Escherichia coli (E. coli)
References: UniProt: P54885, glutamate-5-semialdehyde dehydrogenase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.5865.6
24.3671.6TWO CRYSTALS WERE USED IN THE SOLUTION OF THE STRUCTURE. DATA FROM ONE CRYSTAL WAS USED FOR SE-MET MAD PHASING AND DATA FROM ANOTHER CRYSTAL WAS USED FOR REFINEMENT.
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2771vapor diffusion, sitting drop, nanodrop0.175M Na Cl, 0.06M Acetic Acid, 20.00% MPD, 0.04M Acetate_Na, 0.01M Cymal , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop.175M Na Cl, .06M Acetic Acid, 20% MPD, .04M Acetate_Na, 0.0008M Cymal-6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-110.983966
SYNCHROTRONSSRL BL9-120.97916, 0.97877, 0.90496
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJul 2, 2002flat mirror
MARRESEARCH2IMAGE PLATEJun 23, 2002Flat mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(311) bent monochromatorSINGLE WAVELENGTHMx-ray1
2single crystal Si(311) bent monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9839661
20.979161
30.978771
40.904961
ReflectionResolution: 2.29→47.83 Å / Num. obs: 60572 / % possible obs: 91.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 65.61 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13
Reflection shellResolution: 2.29→2.36 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2500 / % possible all: 51.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.29→47.83 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.483 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO INSUFFICIENT DENSITY, THE FOLLOWING SEGMENTS HAVE NOT BEEN MODELED: CHAIN A 187-188, 254-257, 318-330, 391-412 AND CHAIN B 186-187, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DUE TO INSUFFICIENT DENSITY, THE FOLLOWING SEGMENTS HAVE NOT BEEN MODELED: CHAIN A 187-188, 254-257, 318-330, 391-412 AND CHAIN B 186-187, 254-258, 321-330, 392-413. RAMACHANDRAN OUTLIERS A/B116 AND A334 ARE LOCATED IN WELL DEFINED DENSITY. THE NOMINAL RESOLUTION IS 2.40 A WITH 4140 OBSERVED REFLECTIONS BETWEEN 2.40-2.29 (50 % COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.24782 3075 5.1 %RANDOM
Rwork0.21043 ---
obs0.2123 57462 91.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.733 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20 Å2
2--1.22 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.29→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5912 0 3 124 6039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225979
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9618100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.01326.189244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.362151034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7171518
X-RAY DIFFRACTIONr_chiral_restr0.080.2986
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024368
X-RAY DIFFRACTIONr_nbd_refined0.1920.22417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.217
X-RAY DIFFRACTIONr_mcbond_it2.01734027
X-RAY DIFFRACTIONr_mcangle_it3.46256260
X-RAY DIFFRACTIONr_scbond_it5.59182179
X-RAY DIFFRACTIONr_scangle_it7.886111840
X-RAY DIFFRACTIONr_nbtor_refined0.2940.24122
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1560medium positional0.550.5
1333loose positional0.785
1560medium thermal0.942
1333loose thermal2.5410
LS refinement shellResolution: 2.29→2.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 102 4.42 %
Rwork0.3 2205 -
obs--47.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8006-0.19520.20851.13690.45771.9292-0.0053-0.073-0.0531-0.0659-0.07350.23360.1594-0.40530.0789-0.2103-0.0763-0.0498-0.1485-0.0219-0.0053-16.007122.454926.5354
20.37510.13790.19580.93640.40291.08-0.05270.0094-0.0950.0934-0.02070.234-0.1699-0.2860.0735-0.17510.07930.0446-0.07240.0126-0.0296-16.424270.770534.6224
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 435 / Label seq-ID: 12 - 447

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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