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- PDB-1vkn: Crystal structure of N-acetyl-gamma-glutamyl-phosphate reductase ... -

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Basic information

Entry
Database: PDB / ID: 1vkn
TitleCrystal structure of N-acetyl-gamma-glutamyl-phosphate reductase (TM1782) from Thermotoga maritima at 1.80 A resolution
ComponentsN-acetyl-gamma-glutamyl-phosphate reductase
KeywordsOXIDOREDUCTASE / TM1782 / N-ACETYL-GAMMA-GLUTAMYL-PHOSPHATE REDUCTASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / L-arginine biosynthetic process / NADP+ binding / NAD binding / cytoplasm
Similarity search - Function
: / N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / Semialdehyde dehydrogenase, dimerisation domain / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...: / N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / Semialdehyde dehydrogenase, dimerisation domain / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of N-acetyl-gamma-glutamyl-phosphate reductase (TM1782) from Thermotoga maritima at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 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
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
C: N-acetyl-gamma-glutamyl-phosphate reductase
D: N-acetyl-gamma-glutamyl-phosphate reductase


Theoretical massNumber of molelcules
Total (without water)159,4654
Polymers159,4654
Non-polymers00
Water13,619756
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-94 kcal/mol
Surface area43860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.098, 92.103, 100.880
Angle α, β, γ (deg.)90.00, 112.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-acetyl-gamma-glutamyl-phosphate reductase / AGPR / N-acetyl-glutamate semialdehyde dehydrogenase / NAGSA dehydrogenase


Mass: 39866.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: ARGC, TM1782 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X2A2, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2846.17
22.3146.31
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2951vapor diffusion, sitting drop, nanodrop13.50% PEG 3350, 0.50M (NH4)formate , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 295K
2952vapor diffusion, sitting drop, nanodrop13.50M (NH4)formate, 0.50% PEG 3350 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.2.111
SYNCHROTRONALS 8.2.120.9794, 0.9795, 1.0000
DetectorType: ADSC / Detector: CCD / Date: Sep 20, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
30.97951
ReflectionResolution: 1.8→50 Å / Num. obs: 131126 / % possible obs: 99.46 % / Redundancy: 3.96 % / Biso Wilson estimate: 37.18 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.91
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.12 / Num. unique all: 8413 / % possible all: 95.79

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
autoSHARPphasing
REFMAC5.2.0001refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→46.51 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 7.732 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.117
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. DENSITY FOR TYR 187 IS POOR. 3. LOOPS FROM 178-184 ARE ONLY MODELLED FOR CHAIN A AND B, DENSITIES FOR THEM ARE WEAK. 4. DIFFRACTION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. DENSITY FOR TYR 187 IS POOR. 3. LOOPS FROM 178-184 ARE ONLY MODELLED FOR CHAIN A AND B, DENSITIES FOR THEM ARE WEAK. 4. DIFFRACTION IS ANISOTROPIC. 5. CHAIN D IS FLEXIBLE IN PLACES WHERE THERE ARE NO CRYSTAL CONTACTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21182 6565 5 %RANDOM
Rwork0.17766 ---
obs0.17942 124606 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.956 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å23.77 Å2
2---1.52 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10513 0 0 756 11269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210760
X-RAY DIFFRACTIONr_bond_other_d0.0010.029847
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.96214598
X-RAY DIFFRACTIONr_angle_other_deg0.844322962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47751345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36124.489450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.159151839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6181546
X-RAY DIFFRACTIONr_chiral_restr0.0920.21641
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022069
X-RAY DIFFRACTIONr_nbd_refined0.2070.22015
X-RAY DIFFRACTIONr_nbd_other0.1810.210027
X-RAY DIFFRACTIONr_nbtor_other0.0840.26110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2700
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.211
X-RAY DIFFRACTIONr_mcbond_it2.38436934
X-RAY DIFFRACTIONr_mcbond_other0.65132744
X-RAY DIFFRACTIONr_mcangle_it3.248510874
X-RAY DIFFRACTIONr_scbond_it5.28684396
X-RAY DIFFRACTIONr_scangle_it7.14113724
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 400 4.82 %
Rwork0.274 7903 -
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)
10.60550.0521-0.35340.5177-0.24660.43320.01360.0254-0.05190.1720.09370.1092-0.0744-0.0374-0.1072-0.01210.06160.0194-0.03580.0463-0.033426.15276.661635.5387
20.66780.2833-0.39710.54-0.52270.9255-0.10260.178-0.004-0.03540.1890.05-0.0103-0.1668-0.0864-0.0535-0.0375-0.04440.01330.0536-0.052233.353527.9043-4.3953
30.34220.1569-0.13580.587-0.53890.91240.01680.01940.06060.3185-0.1009-0.1098-0.35450.19110.08410.0999-0.0545-0.0957-0.03070.0049-0.052752.208930.3629.2553
40.84410.1756-0.36370.3278-0.4220.91480.01630.05010.16910.18140.28060.1998-0.5481-0.5563-0.29690.06950.30950.09680.16180.21110.07427.342536.148218.7664
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 33912 - 351
22BB0 - 33912 - 351
33CC1 - 33913 - 351
44DD1 - 33913 - 351

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