[English] 日本語
Yorodumi
- PDB-3ii0: Crystal structure of human Glutamate oxaloacetate transaminase 1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ii0
TitleCrystal structure of human Glutamate oxaloacetate transaminase 1 (GOT1)
ComponentsAspartate aminotransferase, cytoplasmic
KeywordsTRANSFERASE / Glutamate oxaloacetate transaminase 1 / aspartate aminotransferase 1 / pyridoxal phosphate-dependent enzyme / amino acid metabolism / urea and tricarboxylic acid cycles / Structural Genomics / Structural Genomics Consortium / SGC / Aminotransferase / Phosphoprotein / Pyridoxal phosphate
Function / homology
Function and homology information


response to transition metal nanoparticle / Malate-aspartate shuttle / L-glutamate biosynthetic process / L-glutamate catabolic process to aspartate / transdifferentiation / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / Methionine salvage pathway / aspartate biosynthetic process ...response to transition metal nanoparticle / Malate-aspartate shuttle / L-glutamate biosynthetic process / L-glutamate catabolic process to aspartate / transdifferentiation / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / Methionine salvage pathway / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process / glutamate metabolic process / Aspartate and asparagine metabolism / negative regulation of collagen biosynthetic process / carboxylic acid binding / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / 2-oxoglutarate metabolic process / response to carbohydrate / negative regulation of mitochondrial depolarization / negative regulation of cytosolic calcium ion concentration / positive regulation of transforming growth factor beta receptor signaling pathway / response to immobilization stress / fatty acid homeostasis / response to cadmium ion / Notch signaling pathway / axon terminus / response to glucocorticoid / gluconeogenesis / cellular response to mechanical stimulus / cellular response to insulin stimulus / pyridoxal phosphate binding / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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
PYRIDOXAL-5'-PHOSPHATE / D(-)-TARTARIC ACID / Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsUgochukwu, E. / Pilka, E. / Cooper, C. / Bray, J.E. / Yue, W.W. / Muniz, J. / Chaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Ugochukwu, E. / Pilka, E. / Cooper, C. / Bray, J.E. / Yue, W.W. / Muniz, J. / Chaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human Glutamate oxaloacetate transaminase 1 (GOT1)
Authors: Ugochukwu, E. / Pilka, E. / Cooper, C. / Bray, J.E. / Yue, W.W. / Muniz, J. / Chaikuad, A. / Kavanagh, K.L. / Oppermann, U.
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aspartate aminotransferase, cytoplasmic
B: Aspartate aminotransferase, cytoplasmic
C: Aspartate aminotransferase, cytoplasmic
D: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,41925
Polymers191,0234
Non-polymers2,39621
Water13,205733
1
A: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3396
Polymers47,7561
Non-polymers5835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3396
Polymers47,7561
Non-polymers5835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4017
Polymers47,7561
Non-polymers6466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3396
Polymers47,7561
Non-polymers5835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Aspartate aminotransferase, cytoplasmic
D: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,67812
Polymers95,5112
Non-polymers1,16710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint0 kcal/mol
Surface area30330 Å2
MethodPISA
6
B: Aspartate aminotransferase, cytoplasmic
C: Aspartate aminotransferase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,74013
Polymers95,5112
Non-polymers1,22911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint2 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.531, 107.347, 239.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13A
23B
14C
24D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A14 - 213
2115B14 - 213
1215A215 - 410
2215B215 - 410
1125C14 - 213
2125D14 - 213
1225C215 - 410
2225D215 - 410
1136A411 - 417
2136B411 - 417
1146C411 - 417
2146D411 - 417

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein
Aspartate aminotransferase, cytoplasmic / Transaminase A / Glutamate oxaloacetate transaminase 1


Mass: 47755.688 Da / Num. of mol.: 4 / Fragment: UNP residues 14-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOT1 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P17174, aspartate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 0
Details: 0.25M Na_K_tartrate; 15w/v PEG_3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.05→56.04 Å / Num. obs: 127732 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 8.7
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.7 / Num. unique all: 74702 / Rsym value: 0.78 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AJS

1ajs


Resolution: 2.05→56.04 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.293 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.171 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22316 6417 5 %RANDOM
Rwork0.18047 ---
all0.18259 121312 --
obs0.18259 121312 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.762 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2---1.7 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.05→56.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12745 0 156 733 13634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02213312
X-RAY DIFFRACTIONr_bond_other_d0.0010.028977
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.94918105
X-RAY DIFFRACTIONr_angle_other_deg0.937321769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62451648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61423.756623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.419152088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7961587
X-RAY DIFFRACTIONr_chiral_restr0.0860.21965
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022820
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9321.58133
X-RAY DIFFRACTIONr_mcbond_other0.331.53293
X-RAY DIFFRACTIONr_mcangle_it1.607213119
X-RAY DIFFRACTIONr_scbond_it2.78935179
X-RAY DIFFRACTIONr_scangle_it4.0024.54973
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12321MEDIUM POSITIONAL0.060.5
12879LOOSE POSITIONAL0.165
12321MEDIUM THERMAL0.572
12879LOOSE THERMAL0.6910
22323MEDIUM POSITIONAL0.080.5
22899LOOSE POSITIONAL0.165
22323MEDIUM THERMAL0.592
22899LOOSE THERMAL0.6910
384LOOSE POSITIONAL0.575
384LOOSE THERMAL3.2310
481LOOSE POSITIONAL0.225
481LOOSE THERMAL1.6910
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 483 -
Rwork0.287 8782 -
obs--99.32 %
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)
10.8685-0.3872-0.27021.28680.19820.2902-0.0418-0.03980.01090.20090.0373-0.11690.03690.03740.00450.10040.0622-0.00430.05070.01060.015337.2199-6.0572-30.2947
22.51212.3339-3.87716.618-7.8310.0031-0.1556-0.5391-0.08560.04710.0203-0.09390.03950.34390.13530.1984-0.01370.09050.2037-0.01790.064653.9761-14.0687-60.7858
31.0646-0.3260.29811.1033-0.17090.4445-0.0763-0.06420.00110.14880.04250.1575-0.0792-0.07250.03380.05940.04530.01790.04210.0010.03133.0813-48.9168-30.7671
41.33092.39893.50654.81376.77989.6771-0.0127-0.0730.00940.2436-0.07470.12070.2367-0.10840.08740.160.0256-0.01430.18310.01820.1609-14.442-41.9148-62.0321
54.43822.6886.52317.91123.52869.63620.1034-0.047-0.1932-0.07250.1303-0.04790.1853-0.0523-0.23360.12880.05830.03870.13420.04360.154827.0279-71.3159-23.6763
60.7324-0.1339-0.00741.5090.36340.6497-0.0094-0.00540.0639-0.04440.0132-0.3017-0.02040.1242-0.00380.01850.01570.01460.04560.01980.073734.1005-62.1761-38.0092
71.1706-0.03030.22191.3924-0.07080.74310.0295-0.08190.03860.1556-0.0392-0.44510.05350.2120.00970.05390.0355-0.05530.09890.00070.144240.3174-61.9064-26.5362
83.754.51956.28035.49337.580810.54-0.2219-0.0020.1911-0.1203-0.05420.1922-0.29270.06060.27610.3883-0.0074-0.08440.32890.03260.255742.4318-87.7292-16.6056
91.73880.3695-3.26466.5563-4.94889.14460.0005-0.150.16520.12470.05670.0689-0.150.2258-0.05720.17420.0063-0.06670.0899-0.01540.351813.411214.9692-21.3539
100.9188-0.1715-0.18881.3225-0.3030.65380.00740.074-0.0859-0.0162-0.03220.30680.0772-0.10690.02480.06040.02080.01920.0469-0.01860.08945.58426.6543-36.5784
111.4541-0.1139-0.42281.3395-0.00080.74460.0353-0.0552-0.0580.2196-0.04280.4001-0.0413-0.14770.00760.12290.03710.09240.06620.00110.1291-0.0837.3888-24.3127
125.7992-1.1086-0.20421.3973.29418.99420.042-0.7645-1.16890.4541-0.1630.25211.1509-0.90080.12110.47350.02190.0490.32110.1770.4081-0.339435.3822-19.0069
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 409
2X-RAY DIFFRACTION2A410 - 418
3X-RAY DIFFRACTION3B15 - 409
4X-RAY DIFFRACTION4B410 - 418
5X-RAY DIFFRACTION5C13 - 17
6X-RAY DIFFRACTION6C18 - 274
7X-RAY DIFFRACTION7C275 - 409
8X-RAY DIFFRACTION8C410 - 418
9X-RAY DIFFRACTION9D13 - 19
10X-RAY DIFFRACTION10D20 - 274
11X-RAY DIFFRACTION11D275 - 411
12X-RAY DIFFRACTION12D412 - 418

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more