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- PDB-1o20: Crystal structure of Gamma-glutamyl phosphate reductase (TM0293) ... -

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Basic information

Entry
Database: PDB / ID: 1o20
TitleCrystal structure of Gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.00 A resolution
ComponentsGamma-glutamyl phosphate reductase
KeywordsOXIDOREDUCTASE / TM0293 / GAMMA-GLUTAMYL PHOSPHATE REDUCTASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / L-proline biosynthetic process / NADP binding / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.0 A resolution.
Authors: Page, R. / Nelson, M.S. / von Delft, F. / Elsliger, M.A. / Canaves, J.M. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Jaroszewski, L. / ...Authors: Page, R. / Nelson, M.S. / von Delft, F. / Elsliger, M.A. / Canaves, J.M. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Robb, A. / Rodrigues, K. / Schwarzenbacher, R. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL UNIT IS A TETRAMER WITH 222 POINT SYMMETRY, FORMED BY CRYSTALLOGRAPHIC SYMMETRY, AS ADJUDGED BY EXTENSIVE HYDROPHOBIC CONTACTS BETWEEN THESE UNITS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-glutamyl phosphate reductase


Theoretical massNumber of molelcules
Total (without water)48,1231
Polymers48,1231
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Gamma-glutamyl phosphate reductase

A: Gamma-glutamyl phosphate reductase

A: Gamma-glutamyl phosphate reductase

A: Gamma-glutamyl phosphate reductase


Theoretical massNumber of molelcules
Total (without water)192,4944
Polymers192,4944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area17590 Å2
ΔGint-5 kcal/mol
Surface area60230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.150, 111.330, 86.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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


Mass: 48123.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0293 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WYC9, glutamate-5-semialdehyde dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.57 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / pH: 8.4
Details: 15% PEG MME 5000(30%), 0.06M Tris Cl(1M), 0.04M Tris_base(1M), VAPOR DIFFUSION,SITTING DROP,NANODROP, pH 8.40, temperature 293K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8.4 / Method: vapor diffusion, sitting drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 %mPEG50001reservoir
210 mMTris1reservoirpH8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793, 0.9566, 0.9794
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Sep 20, 2002
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.95661
30.97941
ReflectionResolution: 2→50 Å / Num. obs: 34597 / % possible obs: 100 % / Redundancy: 8.55 % / Rsym value: 0.087 / Net I/σ(I): 20.46
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.44 % / Mean I/σ(I) obs: 3.33 / Rsym value: 0.607 / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / % possible obs: 99.3 % / Num. measured all: 295973 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.24refinement
CCP4data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→38.22 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.584 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THERE IS PROMINENT DIFFERENCE DENSITY ATTACHED TO CYS255, POSSIBLY THE RESULT OF PARTIAL OXIDATION, WHICH WAS HOWEVER NOT MODELLED. CNS/O WERE ALSO USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2521 7.6 %RANDOM
Rwork0.16 ---
obs0.163 30837 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2--1.02 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 0 299 3526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213284
X-RAY DIFFRACTIONr_bond_other_d0.0020.023136
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9684440
X-RAY DIFFRACTIONr_angle_other_deg0.84337269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023618
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02638
X-RAY DIFFRACTIONr_nbd_refined0.2020.2663
X-RAY DIFFRACTIONr_nbd_other0.2440.23606
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.22063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.2128
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8161.52059
X-RAY DIFFRACTIONr_mcangle_it1.4923342
X-RAY DIFFRACTIONr_scbond_it2.5531225
X-RAY DIFFRACTIONr_scangle_it4.3214.51098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 137
Rwork0.196 1866
Refinement TLS params.Method: refined / Origin x: 7.6053 Å / Origin y: 41.9533 Å / Origin z: 67.2913 Å
111213212223313233
T0.0831 Å20.0661 Å20.0074 Å2-0.0532 Å20.0111 Å2--0.0414 Å2
L0.7329 °20.0216 °20.0953 °2-0.1585 °20.0582 °2--0.0234 °2
S0.0301 Å °0.1486 Å °-0.1057 Å °-0.0841 Å °-0.037 Å °-0.0131 Å °0.0402 Å °0.0096 Å °0.0069 Å °
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 7.6 % / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 2.07 Å

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