[English] 日本語
Yorodumi
- PDB-4b5v: Crystal structures of divalent metal dependent pyruvate aldolase,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b5v
TitleCrystal structures of divalent metal dependent pyruvate aldolase, HpaI, in complex with 4-hydroxyl-2-ketoheptane-1,7-dioate
Components4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
KeywordsLYASE
Function / homology
Function and homology information


4-hydroxy-2-ketopimelate aldolase activity / 4-hydroxy-2-oxoheptanedioate aldolase / 2,4-dihydroxyhept-2-ene-1,7-dioate aldolase activity / phenylacetate catabolic process / metal ion binding
Similarity search - Function
4-hydroxy-2-oxo-heptane-1,7-dioate aldolase, Enterobacteriales / 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
(4R)-4-oxidanyl-2-oxidanylidene-heptanedioic acid / PYRUVIC ACID / 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase
Similarity search - Component
Biological speciesESCHERICHIA COLI ATCC 8739 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.041 Å
AuthorsCoincon, M. / Wang, W. / Seah, S.Y.K. / Sygusch, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity
Authors: Coincon, M. / Wang, W. / Sygusch, J. / Seah, S.Y.K.
History
DepositionAug 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Atomic model / Database references
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Feb 6, 2013Group: Atomic model
Revision 1.4Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_ptnr1_label_alt_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_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
B: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,80910
Polymers54,0202
Non-polymers7898
Water14,466803
1
A: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
B: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
hetero molecules

A: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
B: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
hetero molecules

A: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
B: 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,42630
Polymers162,0596
Non-polymers2,36824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area26560 Å2
ΔGint-147.2 kcal/mol
Surface area46370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.740, 151.740, 151.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2064-

HOH

21A-2089-

HOH

31A-2134-

HOH

41A-2172-

HOH

51B-2062-

HOH

61B-2087-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE / HPAI / 2 / 4-DIHYDROXYHEPT-2-ENE-1 / 7-DIOIC ACID ALDOLASE / HHED ALDOLASE / 4-HYDROXY-2- ...HPAI / 2 / 4-DIHYDROXYHEPT-2-ENE-1 / 7-DIOIC ACID ALDOLASE / HHED ALDOLASE / 4-HYDROXY-2-KETOHEPTANE-1 / 7-DIOATE ALDOLASE / HKHD ALDOLASE


Mass: 27009.793 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI ATCC 8739 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1IS70, 2-dehydro-3-deoxyglucarate aldolase

-
Non-polymers , 5 types, 811 molecules

#2: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical ChemComp-E8U / (4R)-4-oxidanyl-2-oxidanylidene-heptanedioic acid


Mass: 190.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 803 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsPYR, E8U: MICROHETEROGENEITY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 69.19 % / Description: NONE
Crystal growDetails: 0.5 M AMMONIUM DIHYDROGEN PHOSPHATE, 30% GLYCEROL, 2 MM COCL2 PH 5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→37.9 Å / Num. obs: 72826 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 19.4 % / Biso Wilson estimate: 29.27 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.5
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2 / % possible all: 80.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V5J

2v5j


Resolution: 2.041→37.935 Å / SU ML: 0.24 / σ(F): 2.01 / Phase error: 16.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1792 7093 9.7 %
Rwork0.1532 --
obs0.1557 72812 98.54 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.688 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.041→37.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 52 803 4655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043975
X-RAY DIFFRACTIONf_angle_d0.8685413
X-RAY DIFFRACTIONf_dihedral_angle_d18.4791501
X-RAY DIFFRACTIONf_chiral_restr0.05609
X-RAY DIFFRACTIONf_plane_restr0.003724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0412-2.06440.29891550.28911352X-RAY DIFFRACTION61
2.0644-2.08870.27562310.2442124X-RAY DIFFRACTION97
2.0887-2.11420.26482330.23182168X-RAY DIFFRACTION99
2.1142-2.1410.25852370.21662208X-RAY DIFFRACTION100
2.141-2.16910.22252340.20392228X-RAY DIFFRACTION100
2.1691-2.19880.2182370.18192190X-RAY DIFFRACTION100
2.1988-2.23020.19892380.18022187X-RAY DIFFRACTION100
2.2302-2.26350.22812430.17552247X-RAY DIFFRACTION100
2.2635-2.29890.2022360.17022184X-RAY DIFFRACTION100
2.2989-2.33660.22272380.16082200X-RAY DIFFRACTION100
2.3366-2.37690.19162350.16712204X-RAY DIFFRACTION100
2.3769-2.42010.2182360.16362188X-RAY DIFFRACTION100
2.4201-2.46660.17572410.1592245X-RAY DIFFRACTION100
2.4666-2.5170.18192300.1482205X-RAY DIFFRACTION100
2.517-2.57170.19522430.15292231X-RAY DIFFRACTION100
2.5717-2.63150.17372360.14882196X-RAY DIFFRACTION100
2.6315-2.69730.17682390.15472218X-RAY DIFFRACTION100
2.6973-2.77020.18242350.15372222X-RAY DIFFRACTION100
2.7702-2.85170.18272420.15172216X-RAY DIFFRACTION100
2.8517-2.94370.18422370.1452212X-RAY DIFFRACTION100
2.9437-3.04880.1772430.14732201X-RAY DIFFRACTION100
3.0488-3.17090.17662420.14012241X-RAY DIFFRACTION100
3.1709-3.31510.18132420.14822217X-RAY DIFFRACTION100
3.3151-3.48970.17892360.14342214X-RAY DIFFRACTION100
3.4897-3.70820.14462480.13532243X-RAY DIFFRACTION100
3.7082-3.99420.14752400.12732261X-RAY DIFFRACTION100
3.9942-4.39570.14272400.11662235X-RAY DIFFRACTION100
4.3957-5.03050.13812440.12132249X-RAY DIFFRACTION100
5.0305-6.33310.18022460.15812281X-RAY DIFFRACTION100
6.3331-37.94150.19052560.18182352X-RAY DIFFRACTION100

+
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