[English] 日本語
Yorodumi
- PDB-3bg3: Crystal Structure of Human Pyruvate Carboxylase (missing the biot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bg3
TitleCrystal Structure of Human Pyruvate Carboxylase (missing the biotin carboxylase domain at the N-terminus)
ComponentsPyruvate carboxylase, mitochondrial
KeywordsLIGASE / TIM barrel / ATP-binding / Biotin / Disease mutation / Gluconeogenesis / Lipid synthesis / Manganese / Mitochondrion / Multifunctional enzyme / Nucleotide-binding / Phosphoprotein / Transit peptide
Function / homology
Function and homology information


Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / pyruvate carboxylase / pyruvate carboxylase activity / positive regulation by host of viral process / viral RNA genome packaging / NADP metabolic process / pyruvate metabolic process / Gluconeogenesis / NADH metabolic process ...Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / pyruvate carboxylase / pyruvate carboxylase activity / positive regulation by host of viral process / viral RNA genome packaging / NADP metabolic process / pyruvate metabolic process / Gluconeogenesis / NADH metabolic process / biotin binding / viral release from host cell / gluconeogenesis / lipid metabolic process / mitochondrial matrix / negative regulation of gene expression / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site ...pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / Single hybrid motif / Cyclin A; domain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Homeodomain-like / Aldolase class I / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Aldolase-type TIM barrel / Arc Repressor Mutant, subunit A / TIM Barrel / Roll / Alpha-Beta Barrel / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BTI / : / PYRUVIC ACID / Pyruvate carboxylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsXiang, S. / Tong, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.
Authors: Xiang, S. / Tong, L.
History
DepositionNov 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Pyruvate carboxylase, mitochondrial
B: Pyruvate carboxylase, mitochondrial
C: Pyruvate carboxylase, mitochondrial
D: Pyruvate carboxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,15813
Polymers315,3574
Non-polymers8009
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
MethodPISA
2
A: Pyruvate carboxylase, mitochondrial
D: Pyruvate carboxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1937
Polymers157,6792
Non-polymers5145
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
MethodPISA
3
B: Pyruvate carboxylase, mitochondrial
C: Pyruvate carboxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9656
Polymers157,6792
Non-polymers2864
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.274, 173.321, 118.194
Angle α, β, γ (deg.)90.00, 95.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22D
13A
23D
33A
43D

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAASPASPAA520 - 86060 - 400
211ALAALAASPASPBB520 - 86060 - 400
311ALAALAASPASPCC520 - 86060 - 400
411ALAALAASPASPDD520 - 86060 - 400
112LYSLYSGLUGLUAA1103 - 1178643 - 718
212LYSLYSGLUGLUDD1103 - 1178643 - 718
113GLNGLNLYSLYSAA494 - 51934 - 59
213GLNGLNLYSLYSDD494 - 51934 - 59
323VALVALGLUGLUAA861 - 1097401 - 637
423VALVALGLUGLUDD861 - 1097401 - 637

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Pyruvate carboxylase, mitochondrial / / Pyruvic carboxylase / PCB


Mass: 78839.312 Da / Num. of mol.: 4 / Fragment: CT+PT+BCCP Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: P11498, pyruvate carboxylase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O2S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 90 mM MnCl2, 0.8%(v/v)PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 76525 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.413 / % possible all: 67.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0003refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU B: 40.363 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27129 3915 5.2 %RANDOM
Rwork0.21567 ---
obs0.21852 71717 94.68 %-
all-71717 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.496 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å2-5.79 Å2
2---2.62 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19770 0 43 0 19813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02220255
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9627466
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94952562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41523.977880
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.909153370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8115130
X-RAY DIFFRACTIONr_chiral_restr0.0860.23047
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215486
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.29634
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.213681
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2609
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3751.513100
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.661220594
X-RAY DIFFRACTIONr_scbond_it0.72537906
X-RAY DIFFRACTIONr_scangle_it1.1824.56872
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2602loose positional0.495
12B2602loose positional0.485
13C2602loose positional0.55
14D2602loose positional0.465
21A559loose positional0.875
31A2062loose positional0.665
11A2602loose thermal1.310
12B2602loose thermal1.5110
13C2602loose thermal1.610
14D2602loose thermal1.3510
21A559loose thermal0.810
31A2062loose thermal1.8710
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 228 -
Rwork0.307 3693 -
obs--67.28 %
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)
12.29690.25210.26222.63670.57042.22790.0092-0.3770.31160.0883-0.07750.5404-0.0772-0.55470.0683-0.4066-0.0349-0.063-0.11270.0032-0.1365-17.4815-74.0557-52.2826
22.69521.02450.05273.16810.81942.7440.1212-0.1684-0.06130.3328-0.16820.34770.2664-0.45880.047-0.0932-0.05790.0229-0.21220.0534-0.341123.7925-55.248417.7594
32.6820.93441.49111.39490.14032.9854-0.27340.7020.3539-0.34560.23-0.1694-0.36010.52290.0434-0.1418-0.1833-0.0213-0.14960.1521-0.032438.9685-29.161-9.804
41.9583-0.13590.19310.95730.13034.3512-0.0194-0.162-0.1113-0.07080.1593-0.29690.59830.7275-0.1399-0.11480.17680.0631-0.2718-0.0611-0.28716.0026-97.2982-53.292
550.84170.1383-1.466112.52710.851317.1283-0.1745-0.8198-0.4104-0.4742-0.05480.27040.5666-1.32650.22940.3791-0.1564-0.08280.3983-0.04670.2699-9.6246-56.067410.1344
621.1252-8.7726-1.573427.9499-0.26579.9622-0.6509-0.27280.85961.36790.88970.1537-0.17780.0401-0.23880.4121-0.05740.17580.518-0.17540.307449.2825-63.8438-23.7063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA494 - 109734 - 637
2X-RAY DIFFRACTION2BB494 - 109734 - 637
3X-RAY DIFFRACTION3CC494 - 109734 - 637
4X-RAY DIFFRACTION4DD494 - 109734 - 637
5X-RAY DIFFRACTION5AA1103 - 1178643 - 718
6X-RAY DIFFRACTION6DD1103 - 1178643 - 718

+
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