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- PDB-2g17: The structure of N-acetyl-gamma-glutamyl-phosphate reductase from... -

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Basic information

Entry
Database: PDB / ID: 2g17
TitleThe structure of N-acetyl-gamma-glutamyl-phosphate reductase from Salmonella typhimurium.
ComponentsN-acetyl-gamma-glutamyl-phosphate reductase
KeywordsOXIDOREDUCTASE / N-acetyl-gamma-glutamyl-phosphate reductase / Semialdehyde dehydrogenase / NAD binding domain / amino acid transport metabolism / arginine biosynthesis / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / arginine biosynthetic process / 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 / 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 ...N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / 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
N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsCuff, M.E. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of N-acetyl-gamma-glutamyl-phosphate reductase from Salmonella typhimurium.
Authors: Midwest Center for Structural Genomics (MCSG)
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
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). THE BIOLOGICAL MOLECULE IS UNKNOWN BUT BASED ON THE PQS ANALYSIS IT MAY BE TETRAMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S) AS TETRAMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,35711
Polymers36,3961
Non-polymers96110
Water5,927329
1
A: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)149,42644
Polymers145,5844
Non-polymers3,84340
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
crystal symmetry operation12_555x,x-y,-z+2/31
Buried area18510 Å2
ΔGint-604 kcal/mol
Surface area47980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)165.001, 165.001, 105.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

21A-506-

HOH

DetailsNo experimental data, perhaps dimer (2-x,1-y,z).

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Components

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


Mass: 36395.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: argC / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q8ZKL8, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.708 Å3/Da / Density % sol: 78.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2M (NH4)SO4, 0.1M Tris pH7.0, 0.2M LiSO4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 24, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 37632 / Num. obs: 37632 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXphasing
SOLVEphasing
RESOLVEphasing
DMphasing
CCP4phasing
Cootmodel building
Omodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→49.63 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.298 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.131
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19344 1890 5 %RANDOM
Rwork0.16962 ---
all0.17084 35742 --
obs0.17084 35742 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.292 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0.64 Å20 Å2
2---1.27 Å20 Å2
3---1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 50 329 2934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222691
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9713682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32224.655116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86715408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7661511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21173
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21795
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9091.51735
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33522729
X-RAY DIFFRACTIONr_scbond_it2.33331065
X-RAY DIFFRACTIONr_scangle_it3.5274.5952
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 123 -
Rwork0.195 2532 -
obs--96.13 %
Refinement TLS params.Method: refined / Origin x: 114.5416 Å / Origin y: 53.4859 Å / Origin z: 20.0245 Å
111213212223313233
T-0.2382 Å2-0.053 Å2-0.0133 Å2--0.2366 Å2-0.0491 Å2---0.2019 Å2
L0.732 °20.2812 °2-0.0162 °2-1.4074 °2-0.0577 °2--0.754 °2
S-0.0604 Å °0.1391 Å °-0.1898 Å °-0.1627 Å °0.0574 Å °-0.0819 Å °0.0579 Å °0.0323 Å °0.003 Å °

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