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- PDB-4jbe: 1.95 Angstrom Crystal Structure of Gamma-glutamyl phosphate Reduc... -

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Basic information

Entry
Database: PDB / ID: 4jbe
Title1.95 Angstrom Crystal Structure of Gamma-glutamyl phosphate Reductase from Saccharomonospora viridis.
ComponentsGamma-glutamyl phosphate reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / gamma-glutamyl phosphate reductase / NAD(P)
Function / homology
Function and homology information


glutamate-5-semialdehyde dehydrogenase activity / proline biosynthetic process / NADP binding / metal ion binding
Similarity search - Function
Glutamate-5-semialdehyde dehydrogenase / 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 ...Glutamate-5-semialdehyde dehydrogenase / 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
BETA-MERCAPTOETHANOL / Gamma-glutamyl phosphate reductase
Similarity search - Component
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Filippova, E.V. / Halavaty, A. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: 1.95 Angstrom Crystal Structure of Gamma-glutamyl phosphate Reductase from Saccharomonospora viridis.
Authors: Minasov, G. / Filippova, E.V. / Halavaty, A. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)97,45929
Polymers96,0242
Non-polymers1,43527
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8280 Å2
ΔGint-188 kcal/mol
Surface area31960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.510, 55.118, 64.246
Angle α, β, γ (deg.)90.00, 91.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-501-

CA

DetailsChains A and B represent Biological Assembly.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Gamma-glutamyl phosphate reductase


Mass: 48012.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Strain: DSM 43017 / Gene: proA, Svir_28610 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: C7MW73

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Non-polymers , 6 types, 643 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein: 8.3mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PACT (B11), 0.2M Calcium chloride, 0.1M MES pH 6.0, 20% (w/v) PEG 6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 30, 2013 / Details: Beryllium lenses
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 67453 / Num. obs: 67453 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3341 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O20

1o20


Resolution: 1.95→29.73 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.31 / SU ML: 0.069
Isotropic thermal model: Thermal Factors Isotropically Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20836 3417 5.1 %RANDOM
Rwork0.16797 ---
all0.17004 64036 --
obs0.17004 64036 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.695 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.99 Å2
2--2.86 Å20 Å2
3----2.53 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6163 0 58 616 6837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226510
X-RAY DIFFRACTIONr_bond_other_d0.0010.024401
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9888898
X-RAY DIFFRACTIONr_angle_other_deg0.86310699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9375866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.18722.958284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.243151039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0071577
X-RAY DIFFRACTIONr_chiral_restr0.0820.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021302
X-RAY DIFFRACTIONr_mcbond_it0.9561.54232
X-RAY DIFFRACTIONr_mcbond_other0.3121.51710
X-RAY DIFFRACTIONr_mcangle_it1.63126808
X-RAY DIFFRACTIONr_scbond_it2.96532278
X-RAY DIFFRACTIONr_scangle_it4.6734.52090
LS refinement shellResolution: 1.954→2.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 234 -
Rwork0.234 4600 -
obs-4600 97.81 %
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)
11.1920.21190.21550.83960.36981.5763-0.02990.0095-0.0078-0.07780.0071-0.0614-0.1248-0.08920.02280.10160.02540.00210.0330.00650.047349.886816.085728.1892
21.1925-0.09160.0471.099-0.32920.8427-0.00020.0466-0.0061-0.04470.0084-0.02050.03490.0043-0.00820.08270.00470.00340.0043-0.01160.063360.91013.908858.7891
32.195-0.38-1.06440.45250.50161.90140.0863-0.0293-0.1531-0.029-0.00210.01420.0241-0.1928-0.08430.08120.0105-0.02170.0907-0.00280.050344.36639.876444.1575
43.429-0.6465-1.05332.1109-0.02941.6837-0.02090.156-0.2579-0.06210.04830.31370.2375-0.3363-0.02730.0962-0.0156-0.03720.2856-0.01860.108220.232515.574739.6763
50.98060.0586-0.35281.2981-0.4951.75490.0742-0.1270.13370.15780.04420.0177-0.2022-0.1243-0.11840.09970.0547-0.00070.1854-0.04470.072530.557728.837866.3184
62.6134-0.60490.99321.29910.0692.2017-0.04210.14470.24830.0053-0.0275-0.0148-0.1665-0.1290.06960.02890.0509-0.01050.2869-0.00430.080115.320535.010235.8175
72.0303-1.0988-0.01151.03340.9041.89950.0319-0.1210.0708-0.0257-0.0057-0.02740.0278-0.2113-0.02620.12320.0332-0.01920.2448-0.0040.08927.031621.737450.2737
82.4402-1.4713-0.20384.06860.26012.1899-0.0010.014-0.28380.07740.00280.20880.1732-0.2939-0.00180.0991-0.0471-0.01680.049-0.00540.107441.24510.869654.3882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 96
2X-RAY DIFFRACTION1A118 - 232
3X-RAY DIFFRACTION2A233 - 372
4X-RAY DIFFRACTION3A373 - 401
5X-RAY DIFFRACTION4A97 - 117
6X-RAY DIFFRACTION4A402 - 413
7X-RAY DIFFRACTION5B2 - 96
8X-RAY DIFFRACTION5B118 - 232
9X-RAY DIFFRACTION6B233 - 372
10X-RAY DIFFRACTION7B373 - 401
11X-RAY DIFFRACTION8B97 - 117
12X-RAY DIFFRACTION8B402 - 413

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