[English] 日本語
Yorodumi
- PDB-4mfd: Structure of the carboxyl transferase domain from Rhizobium etli ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mfd
TitleStructure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxalate
ComponentsPYRUVATE CARBOXYLASE
KeywordsLIGASE / TIM Barrel
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding / 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. ...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 synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Cyclin A; domain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Homeodomain-like / Aldolase class I / Carbamoyl-phosphate synthase subdomain signature 2. / Aldolase-type TIM barrel / Arc Repressor Mutant, subunit A / TIM Barrel / Alpha-Beta Barrel / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
OXALATE ION / Pyruvate carboxylase
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLietzan, A.D. / St.Maurice, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogs.
Authors: Lietzan, A.D. / St.Maurice, M.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PYRUVATE CARBOXYLASE
B: PYRUVATE CARBOXYLASE
C: PYRUVATE CARBOXYLASE
D: PYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,89022
Polymers279,8544
Non-polymers1,03718
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.657, 157.368, 244.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999051, 0.039113, 0.019151), (0.033605, 0.972072, -0.232264), (-0.027701, -0.2314, -0.972464)80.71976, 69.03878, 597.84326
3given(-0.560163, 0.089435, 0.82354), (0.05871, -0.987369, 0.147161), (0.826299, 0.130784, 0.547837)-181.30305, -3.27092, 96.95734
4given(0.548512, -0.136787, -0.824878), (-0.109839, -0.989766, 0.091092), (-0.828897, 0.040639, -0.557923)269.18262, 21.01823, 503.08987

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
PYRUVATE CARBOXYLASE


Mass: 69963.375 Da / Num. of mol.: 4
Fragment: CARBOXYL TRANSFERASE DOMAIN, UNP residues 465-1067
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / Gene: pyc, RHE_CH04002 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2K340, pyruvate carboxylase

-
Non-polymers , 6 types, 208 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 298 K / Method: batch crystallization under oil / pH: 6
Details: 11.3% (w/v) PEG 8000, 99 mM BisTris (pH 6.0), 346 mM tetramethylammonium chloride, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 108391 / Num. obs: 108188 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.1
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 4.4 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
MD2diffractometer software from EMBLdata collection
PHASERphasing
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JX4

4jx4


Resolution: 2.55→48.26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 20.046 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23951 5409 5 %RANDOM
Rwork0.19283 ---
obs0.1952 102898 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.346 Å2
Baniso -1Baniso -2Baniso -3
1-8.57 Å20 Å20 Å2
2---4.64 Å20 Å2
3----3.93 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17794 0 48 190 18032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01918280
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216802
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.96724855
X-RAY DIFFRACTIONr_angle_other_deg0.869338538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61752390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24724.11747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.028152727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.43515105
X-RAY DIFFRACTIONr_chiral_restr0.0860.22818
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02121095
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024022
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_it1.6582.6299551
X-RAY DIFFRACTIONr_mcbond_other1.6582.6299550
X-RAY DIFFRACTIONr_mcangle_it2.6173.94211932
X-RAY DIFFRACTIONr_mcangle_other2.6173.94211933
X-RAY DIFFRACTIONr_scbond_it2.3412.7158729
X-RAY DIFFRACTIONr_scbond_other2.3162.7068709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.634412896
X-RAY DIFFRACTIONr_long_range_B_refined5.7421.24220928
X-RAY DIFFRACTIONr_long_range_B_other5.73821.23120923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.547→2.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 395 -
Rwork0.262 7074 -
obs-7074 93.93 %
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)
10.6421-0.09140.00282.5817-0.81611.37810.0004-0.0686-0.04210.16520.05950.03050.32690.0641-0.05990.14310.0118-0.02750.16640.00290.152937.683.2465260.7041
20.91410.4780.63651.98850.17992.2609-0.0915-0.09340.1037-0.04130.10160.2113-0.2002-0.5381-0.01010.32280.1732-0.02170.41930.01520.225750.306812.2466342.3853
32.0683-1.0751.18684.1543-0.21381.7961-0.6768-0.7283-0.23861.75860.84220.7288-0.7129-0.6441-0.16540.99590.51680.34110.49090.26280.402713.468334.8117270.0933
41.1811-0.11020.69752.5001-0.34912.22040.07170.1942-0.0006-0.9002-0.079-0.6432-0.39560.46260.00730.98290.02480.1710.3466-0.07480.475675.314439.6249325.4341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A471 - 1067
2X-RAY DIFFRACTION1A1101 - 1105
3X-RAY DIFFRACTION2B471 - 1067
4X-RAY DIFFRACTION2B1101 - 1105
5X-RAY DIFFRACTION3C471 - 1067
6X-RAY DIFFRACTION3C1101 - 1104
7X-RAY DIFFRACTION4D471 - 1067
8X-RAY DIFFRACTION4D1101 - 1104

+
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