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- PDB-4k30: Structure of the N-acetyltransferase domain of human N-acetylglut... -

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Basic information

Entry
Database: PDB / ID: 4k30
TitleStructure of the N-acetyltransferase domain of human N-acetylglutamate synthase
ComponentsN-acetylglutamate synthase, mitochondrial
KeywordsTRANSFERASE / GCN5-ralated N-acetyltransferase fold / synthase
Function / homology
Function and homology information


methione N-acyltransferase activity / amino-acid N-acetyltransferase / acetyl-CoA:L-glutamate N-acetyltransferase activity / Urea cycle / glutamate metabolic process / urea cycle / arginine biosynthetic process / arginine binding / mitochondrial matrix / phosphorylation / mitochondrion
Similarity search - Function
N-acetylglutamate synthase, animal / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain / NAT, N-acetyltransferase, of N-acetylglutamate synthase / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain profile. / Acetylglutamate kinase-like superfamily / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-ACETYL-L-GLUTAMATE / N-acetylglutamate synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.103 Å
AuthorsShi, D. / Zhao, G. / Jin, Z. / Allewell, N.M. / Tuchman, M.
CitationJournal: Plos One / Year: 2013
Title: Crystal structure of the N-acetyltransferase domain of human N-acetyl-L-glutamate synthase in complex with N-acetyl-L-glutamate provides insights into its catalytic and regulatory mechanisms.
Authors: Zhao, G. / Jin, Z. / Allewell, N.M. / Tuchman, M. / Shi, D.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylglutamate synthase, mitochondrial
B: N-acetylglutamate synthase, mitochondrial
X: N-acetylglutamate synthase, mitochondrial
Y: N-acetylglutamate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0408
Polymers73,2834
Non-polymers7574
Water4,792266
1
A: N-acetylglutamate synthase, mitochondrial
B: N-acetylglutamate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0204
Polymers36,6422
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-13 kcal/mol
Surface area15440 Å2
MethodPISA
2
X: N-acetylglutamate synthase, mitochondrial
hetero molecules

X: N-acetylglutamate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0204
Polymers36,6422
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_667-y+1,-x+1,-z+5/21
Buried area1550 Å2
ΔGint-14 kcal/mol
Surface area14900 Å2
MethodPISA
3
Y: N-acetylglutamate synthase, mitochondrial
hetero molecules

Y: N-acetylglutamate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0204
Polymers36,6422
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_467y-1,x+1,-z+21
Buried area1440 Å2
ΔGint-12 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.141, 116.141, 109.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-729-

HOH

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Components

#1: Protein
N-acetylglutamate synthase, mitochondrial / Amino-acid acetyltransferase / N-acetylglutamate synthase long form / N-acetylglutamate synthase ...Amino-acid acetyltransferase / N-acetylglutamate synthase long form / N-acetylglutamate synthase short form / N-acetylglutamate synthase conserved domain form


Mass: 18320.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAGS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N159, amino-acid N-acetyltransferase
#2: Chemical
ChemComp-NLG / N-ACETYL-L-GLUTAMATE


Mass: 189.166 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H11NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.52 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-tris, pH 6.5, 35% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 44139 / Num. obs: 44139 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.093 / Χ2: 1.276 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.149.70.90121501.048199.8
2.14-2.18110.78921601.1021100
2.18-2.2212.10.70421891.0891100
2.22-2.2612.80.68221491.091100
2.26-2.3113.30.58421931.1031100
2.31-2.3713.80.52721601.1181100
2.37-2.4214.30.47921921.1441100
2.42-2.4914.70.41121711.1781100
2.49-2.5614.80.34921951.2141100
2.56-2.6514.80.28421661.3611100
2.65-2.7414.80.2322051.3891100
2.74-2.8514.80.20221951.5921100
2.85-2.9814.70.16222001.6761100
2.98-3.1414.70.13222001.6091100
3.14-3.3314.50.10222051.7871100
3.33-3.5914.10.08222091.5231100
3.59-3.9513.70.07522471.3571100
3.95-4.5213.30.0622421.1371100
4.52-5.713.40.05122930.9531100
5.7-5012.60.04324180.773199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3S6H

3s6h


Resolution: 2.103→38.458 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8226 / SU ML: 0.25 / σ(F): 1.34 / σ(I): 0 / Phase error: 24.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1994 4.53 %Random
Rwork0.1847 ---
all0.1874 44139 --
obs0.1873 44051 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.27 Å2 / Biso mean: 55.433 Å2 / Biso min: 18.56 Å2
Refinement stepCycle: LAST / Resolution: 2.103→38.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 0 52 266 5281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085149
X-RAY DIFFRACTIONf_angle_d1.1036955
X-RAY DIFFRACTIONf_chiral_restr0.077715
X-RAY DIFFRACTIONf_plane_restr0.004893
X-RAY DIFFRACTIONf_dihedral_angle_d12.8741873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1026-2.15520.31511260.25252867299397
2.1552-2.21340.27831510.228729403091100
2.2134-2.27850.29651410.224529833124100
2.2785-2.35210.31721350.211129623097100
2.3521-2.43610.25411400.202129703110100
2.4361-2.53370.25741450.207729863131100
2.5337-2.64890.2921440.199229573101100
2.6489-2.78860.26371320.197930133145100
2.7886-2.96320.23671470.205729913138100
2.9632-3.19190.25181420.197430103152100
3.1919-3.51290.25161450.176230223167100
3.5129-4.02080.2241460.162730443190100
4.0208-5.06390.19311420.149730883230100
5.0639-38.46450.25551580.19383224338299
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)
13.35660.21580.24494.2032-0.33683.6828-0.04570.12360.08890.1081-0.1023-0.3853-0.05180.29790.16990.24280.00580.00770.26440.02230.211149.1075123.4552115.4275
24.3545-3.01750.02776.62460.17324.18930.04920.0124-0.22620.1219-0.11210.4844-0.0111-0.61760.04480.23250.0018-0.02240.29050.00340.2333.358125.9875117.3562
35.12050.1514-0.43084.3472-0.58417.12240.1316-0.96560.06590.47280.15660.18230.2328-0.5321-0.22050.43260.01150.06580.7203-0.05730.397312.01133.0743139.1689
44.5689-1.1543-1.50476.73642.30236.69340.2664-0.48480.47610.0308-0.069-0.1172-0.40080.1468-0.15190.33040.03640.03440.394-0.03930.276423.1702136.1023128.1028
53.41171.1871-0.53945.9821-1.63753.7553-0.15190.12190.16610.28350.05240.2734-0.0325-0.01580.13160.32870.06260.09070.23040.07950.260545.2192100.4168129.1558
63.71491.97560.13335.8011-1.34653.05840.0003-0.2656-0.14560.5239-0.0247-0.0287-0.0969-0.01390.03880.51490.13920.11980.37250.14190.319741.555387.4441137.5778
74.0286-0.4872-0.44596.65440.63765.3521-0.29440.6815-1.6814-0.6270.6229-1.5670.31770.4265-0.24480.6551-0.02120.07330.5898-0.12521.296118.2942105.5498100.6638
88.7678-0.93951.07768.87661.40267.6001-0.1037-0.5088-0.32470.2270.4259-0.67950.3980.2768-0.27860.5482-0.0913-0.06360.48710.12830.67935.2567109.7057109.3771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 375:469A375 - 469
2X-RAY DIFFRACTION2chain A and resid 470:527A470 - 527
3X-RAY DIFFRACTION3chain B and resid 376:469B376 - 469
4X-RAY DIFFRACTION4chain B and resid 470:527B470 - 527
5X-RAY DIFFRACTION5chain X and resid 375:469X375 - 469
6X-RAY DIFFRACTION6chain X and resid 470:527X470 - 527
7X-RAY DIFFRACTION7chain Y and resid 377:469Y377 - 469
8X-RAY DIFFRACTION8chain Y and resid 470:525Y470 - 525

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