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- PDB-2ozp: Crystal structure of N-acetyl-gamma-glutamyl-phosphate reductase ... -

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Basic information

Entry
Database: PDB / ID: 2ozp
TitleCrystal structure of N-acetyl-gamma-glutamyl-phosphate reductase (TTHA1904) from Thermus thermophilus
ComponentsN-acetyl-gamma-glutamyl-phosphate reductase
KeywordsOXIDOREDUCTASE / Amino acid biosynthesis / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


[amino-group carrier protein]-6-phospho-L-2-aminoadipate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / lysine biosynthetic process via aminoadipic acid / arginine biosynthetic process / NAD binding / protein dimerization activity / cytoplasm
Similarity search - Function
[LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase / 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 ...[LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase / 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
AZIDE ION / [LysW]-L-2-aminoadipate 6-phosphate reductase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsRehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of N-acetyl-gamma-glutamyl-phosphate reductase (TTHA1904) from Thermus thermophilus
Authors: Rehse, P.H. / Yokoyama, S.
History
DepositionFeb 27, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 25, 2017Group: Refinement description / Category: refine_ls_shell / Item: _refine_ls_shell.percent_reflns_obs

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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)38,77110
Polymers38,2841
Non-polymers4869
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)155,08240
Polymers153,1374
Non-polymers1,94536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Buried area23000 Å2
ΔGint-191 kcal/mol
Surface area45830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.957, 144.957, 85.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1094-

HOH

21A-1271-

HOH

31A-1282-

HOH

41A-1294-

HOH

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Components

#1: Protein N-acetyl-gamma-glutamyl-phosphate reductase


Mass: 38284.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3)
References: UniProt: Q5SH26, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 80mM Sodium Hepes, 1.6% PEG 400, 1.6M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97882, 0.97935, 0.90000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2006 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978821
20.979351
30.91
Reflection

Χ2: 1 / D res low: 50 Å / % possible obs: 100

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsD res high (Å)Num. obs
21.3113.37560850.0912.0135565
21.2213.16536270.0872.1130890
21.2312.56711620.0892.0931716
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.335010010.048118.7
3.444.3310010.048120.5
33.4410010.065121
2.73310010.1121.4
2.532.7310010.126121.6
2.382.5310010.173121.8
2.262.3810010.232121.9
2.172.2610010.283122
2.082.1710010.401122
2.012.0810010.489122
4.545010020.042118.4
3.614.5410020.043120.4
3.153.6110020.056120.9
2.863.1510020.09121.3
2.662.8610020.134121.5
2.52.6610020.164121.7
2.382.510020.232121.8
2.272.3810020.299121.9
2.192.2710020.37121.9
2.112.1910020.498122
4.55010030.043118.3
3.574.510030.043120.3
3.123.5710030.057120.9
2.843.1210030.094121.3
2.632.8410030.135121.6
2.482.6310030.167121.7
2.352.4810030.234121.9
2.252.3510030.3122
2.162.2510030.35122
2.092.1610030.486122
ReflectionResolution: 2.01→126 Å / Num. all: 35565 / Num. obs: 64827 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.3 % / Rmerge(I) obs: 0.091 / Χ2: 1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 22 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 7.9 / Num. unique all: 3480 / Χ2: 1 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97884.36-4.98
13 wavelength20.92.87-4.42
13 wavelength30.97932.52-10.12
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se27.6050.4740.4150.1040.969
2Se12.2530.540.4670.0680.841
Phasing dmFOM : 0.69 / FOM acentric: 0.69 / FOM centric: 0.67 / Reflection: 35530 / Reflection acentric: 31104 / Reflection centric: 4426
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-47.4480.960.970.9317011171530
3.6-5.70.940.960.8948434000843
2.9-3.60.870.880.859835195788
2.5-2.90.760.770.6559425283659
2.2-2.50.580.590.491054495111033
2-2.20.350.360.2765175944573

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.01→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3227 4.8 %random
Rwork0.185 ---
all0.185 64827 --
obs0.185 35565 97.3 %-
Solvent computationBsol: 52.206 Å2
Displacement parametersBiso mean: 27.346 Å2
Baniso -1Baniso -2Baniso -3
1--3.387 Å2-1.533 Å20 Å2
2---3.387 Å20 Å2
3---6.774 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 31 301 3002
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0071761.5
X-RAY DIFFRACTIONc_angle_d1.540882
X-RAY DIFFRACTIONc_dihedral_angle_d24.937282
X-RAY DIFFRACTIONc_improper_angle_d0.934562.5
LS refinement shellResolution: 2.01→2.08 Å
RfactorNum. reflection% reflection
Rfree0.3125 325 -
Rwork0.2401 --
obs-6216 93.65 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4lig.param

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