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- PDB-2i3g: Crystal structure of N-Acetyl-gamma-Glutamyl-Phosphate Reductase ... -

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Basic information

Entry
Database: PDB / ID: 2i3g
TitleCrystal structure of N-Acetyl-gamma-Glutamyl-Phosphate Reductase (Rv1652) from Mycobacterium tuberculosis in complex with NADP+.
ComponentsN-acetyl-gamma-glutamyl-phosphate reductase
KeywordsOXIDOREDUCTASE / dimer interface beta sandwich / dimer / Rossmann fold / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / TB Structural Genomics Consortium / TBSGC
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 / protein dimerization activity / 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, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain ...: / 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, 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCherney, L.T. / Cherney, M.M. / Garen, C.R. / Moraidin, F. / James, M.N.G. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB) / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of N-acetyl-gamma-glutamyl-phosphate Reductase from Mycobacterium tuberculosis in Complex with NADP(+).
Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / Niu, C. / Moradian, F. / James, M.N.G.
History
DepositionAug 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL UNIT HAS BEEN CORRECTED BY TRANSLATING CHAIN A WITH SYMMETRY OPERATOR -X,Y,-Z.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5886
Polymers72,6822
Non-polymers1,9054
Water12,394688
1
A: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2943
Polymers36,3411
Non-polymers9532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2943
Polymers36,3411
Non-polymers9532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules

A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,17512
Polymers145,3654
Non-polymers3,8118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20330 Å2
ΔGint-92 kcal/mol
Surface area43220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)141.456, 78.214, 88.034
Angle α, β, γ (deg.)90.00, 127.46, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biologycal assembly is a dimer. There are two half-dimers in the asymmetric unit.

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Components

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


Mass: 36341.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: argC / Plasmid: pDEST15-1652 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P63562, UniProt: P9WPZ9*PLUS, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 17% PEG 10000, 0.1 M Bis-Tris pH 5.5, 0.1 M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2006
RadiationMonochromator: single wavelength / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 65308 / Num. obs: 59626 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.92 Å / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1vkn

1vkn


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.637 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20498 2956 5 %RANDOM
Rwork0.1612 ---
all0.16336 62226 --
obs0.16336 56669 91.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.308 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.26 Å2
2--0.64 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 124 688 5832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215309
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.997287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70422.124193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60615732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8611544
X-RAY DIFFRACTIONr_chiral_restr0.0960.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024016
X-RAY DIFFRACTIONr_nbd_refined0.1970.22540
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2582
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.252
X-RAY DIFFRACTIONr_mcbond_it0.7821.53509
X-RAY DIFFRACTIONr_mcangle_it1.29825505
X-RAY DIFFRACTIONr_scbond_it2.00432005
X-RAY DIFFRACTIONr_scangle_it3.2194.51782
LS refinement shellResolution: 1.85→1.894 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 188 -
Rwork0.242 3684 -
obs-3684 80.55 %

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