[English] 日本語
Yorodumi
- PDB-4jx6: Structure of the carboxyl transferase domain Y628A from Rhizobium... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jx6
TitleStructure of the carboxyl transferase domain Y628A from Rhizobium etli pyruvate carboxylase with pyruvate
ComponentsPyruvate carboxylase
KeywordsLigase / transferase / TIM Barrel
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding
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 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 / Cyclin A; domain 1 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Homeodomain-like / Aldolase class I / Carbamoyl-phosphate synthase subdomain signature 2. / Arc Repressor Mutant, subunit A / Aldolase-type TIM barrel / TIM Barrel / Roll / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PYRUVIC ACID / Pyruvate carboxylase
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsLietzan, A.D. / St Maurice, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: A Substrate-induced Biotin Binding Pocket in the Carboxyltransferase Domain of Pyruvate Carboxylase.
Authors: Lietzan, A.D. / St Maurice, M.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Sep 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _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)280,11215
Polymers279,4854
Non-polymers62711
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pyruvate carboxylase
C: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1028
Polymers139,7432
Non-polymers3606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-13 kcal/mol
Surface area43100 Å2
MethodPISA
3
B: Pyruvate carboxylase
D: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,0107
Polymers139,7432
Non-polymers2675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-15 kcal/mol
Surface area43170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.809, 157.280, 245.885
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(0.998164, -0.059486, -0.011376), (-0.054923, -0.968238, 0.243923), (-0.025524, -0.242851, -0.969728)40.58052, 11.04476, -6.78721
3given(-0.581692, -0.087225, 0.808719), (0.05866, 0.987147, 0.148662), (-0.811291, 0.133915, -0.569098)-52.72989, 47.76824, -37.61703
4given(-0.571268, 0.160177, 0.804982), (0.130366, 0.986029, -0.103686), (-0.810344, 0.04571, -0.584169)-39.30542, -39.08739, -52.19997

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyruvate carboxylase


Mass: 69871.281 Da / Num. of mol.: 4 / Mutation: Y628A
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 , 5 types, 71 molecules

#2: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 298 K / pH: 6
Details: 11.7% (w/v) PEG 8000, 100 mM BisTris (pH 6.0), 200 mM Tetramethylammonium chloride, 3% (v/v) glycerol, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. all: 83991 / Num. obs: 83911 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 26.3
Reflection shellResolution: 2.78→2.83 Å / Redundancy: 7 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.3 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
MD2diffractometer software from EMBLdata collection
PHASERphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7

2qf7


Resolution: 2.78→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 32.99 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.764 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25844 4189 5 %RANDOM
Rwork0.20894 ---
obs0.21147 79718 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.618 Å2
Baniso -1Baniso -2Baniso -3
1-8.91 Å20 Å20 Å2
2---2.29 Å20 Å2
3----6.63 Å2
Refinement stepCycle: LAST / Resolution: 2.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17245 0 26 60 17331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217646
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.96224118
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90852352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98624.296696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.043152463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0711586
X-RAY DIFFRACTIONr_chiral_restr0.0910.22778
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113634
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.775→2.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 281 -
Rwork0.319 5447 -
obs--98.78 %
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)
10.5151-0.0440.14031.4887-0.91641.9173-0.0161-0.1252-0.0366-0.37030.0424-0.00190.5933-0.0082-0.02640.26370.00610.02110.08510.03580.1546-89.5263.1172-106.6786
21.29170.34061.50971.13740.123.7544-0.2502-0.27630.20240.52650.12510.0973-0.4849-0.96680.12510.44720.3066-0.04880.5452-0.04710.2143-77.505712.1591-25.0533
31.7674-0.94221.39252.9413-0.97412.9051-0.6051-0.8207-0.03021.00280.79960.4011-0.7018-0.9606-0.19450.42170.42180.09070.65760.15870.3019-113.629434.8058-97.7619
41.093-0.31320.53782.226-0.27912.46020.0550.18080.0238-0.3865-0.1368-0.5759-0.54650.43660.08180.72240.061-0.15480.3872-0.10690.5714-52.12739.2809-42.0526
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A471 - 1067
2X-RAY DIFFRACTION2B471 - 1067
3X-RAY DIFFRACTION3C471 - 1067
4X-RAY DIFFRACTION4D471 - 1067

+
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