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- PDB-1gbn: HUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GA... -

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Basic information

Entry
Database: PDB / ID: 1gbn
TitleHUMAN ORNITHINE AMINOTRANSFERASE COMPLEXED WITH THE NEUROTOXIN GABACULINE
ComponentsORNITHINE AMINOTRANSFERASE
KeywordsTRANSFERASE / ORNITHINE AMINOTRANSFERASE / UREA CYCLE / PYRIDOXAL-5'-PHOSPHATE
Function / homology
Function and homology information


L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...L-arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / L-arginine catabolic process to L-glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-AMINOBENZOIC ACID / GABACULINE / PYRIDOXAL-5'-PHOSPHATE / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShah, S.A. / Shen, B.W. / Brunger, A.T.
CitationJournal: Structure / Year: 1997
Title: Human ornithine aminotransferase complexed with L-canaline and gabaculine: structural basis for substrate recognition.
Authors: Shah, S.A. / Shen, B.W. / Brunger, A.T.
History
DepositionMay 29, 1997Processing site: BNL
Revision 1.0Jun 3, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2799
Polymers134,1183
Non-polymers1,1616
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1856
Polymers89,4122
Non-polymers7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-52 kcal/mol
Surface area24800 Å2
MethodPISA
3
C: ORNITHINE AMINOTRANSFERASE
hetero molecules

C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1896
Polymers89,4122
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12320 Å2
ΔGint-50 kcal/mol
Surface area24830 Å2
MethodPISA
4
C: ORNITHINE AMINOTRANSFERASE
hetero molecules

A: ORNITHINE AMINOTRANSFERASE
B: ORNITHINE AMINOTRANSFERASE
C: ORNITHINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,37412
Polymers178,8254
Non-polymers1,5498
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_555y,x,-z1
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)115.013, 115.013, 185.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.905265, 0.049533, -0.421949), (0.048561, -0.998735, -0.013059), (-0.422062, -0.008668, -0.906526)7.61656, 73.34723, 43.01362
2given(-0.440738, 0.789615, 0.426917), (-0.872489, -0.488624, 0.003011), (0.21098, -0.371153, 0.904286)-2.00252, 80.59359, -6.71558

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Components

#1: Protein ORNITHINE AMINOTRANSFERASE


Mass: 44706.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: BOUND INHIBITOR GABACULINE / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical ChemComp-GAB / 3-AMINOBENZOIC ACID / GABACULINE


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-GBC / GABACULINE


Mass: 141.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO2
#5: Water ChemComp-HOH / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
250 mMTris-HCl1drop
30.01 MPLP1drop
410-15 %PEG60001reservoir
550-200 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9417
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 10, 1995 / Details: DUEL SLITS
RadiationMonochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9417 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 57010 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.17 / % possible all: 80.1
Reflection
*PLUS
% possible obs: 89.9 %
Reflection shell
*PLUS
Lowest resolution: 2.4 Å / % possible obs: 80.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.171

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAT

1oat


Resolution: 2.3→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 470426.53 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 5275 10.1 %RANDOM
Rwork0.209 ---
obs0.209 52216 81.9 %-
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20.12 Å20 Å2
2--1.3 Å20 Å2
3----2.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9450 0 75 329 9854
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.421.5
X-RAY DIFFRACTIONx_mcangle_it2.232
X-RAY DIFFRACTIONx_scbond_it2.342
X-RAY DIFFRACTIONx_scangle_it3.342.5
Refine LS restraints NCSRms dev Biso : 1.618 Å2 / Rms dev position: 0.1647 Å
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 705 10.1 %
Rwork0.265 6270 -
obs--66.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.PLP
X-RAY DIFFRACTION3PARAM.GABACULINE
X-RAY DIFFRACTION4PARAM.PATCH
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 52218 / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.32
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Num. reflection Rfree: 70 / % reflection Rfree: 10 % / Num. reflection Rwork: 5123

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