[English] 日本語
Yorodumi
- PDB-7etc: Crystal structure of AbHpaI-Zn-(4R)-KDGal complex, Class II aldol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7etc
TitleCrystal structure of AbHpaI-Zn-(4R)-KDGal complex, Class II aldolase, HpaI from Acinetobacter baumannii
Components4-hydroxy-2-oxoheptanedioate aldolase
KeywordsLYASE / TIM barrel / aldehyde lyase
Function / homology
Function and homology information


: / 4-hydroxy-2-oxoheptanedioate aldolase / phenylacetate catabolic process / metal ion binding
Similarity search - Function
2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
Chem-JBU / PYRUVIC ACID / 4-hydroxy-2-oxoheptanedioate aldolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
Model detailsCrystal structure of AbHpaI-Zn-pyruvate complex, a class II aldolase, HpaI from Acinetobacter baumannii
AuthorsWatthaisong, P. / Binlaeh, A. / Jaruwat, A. / Chaiyen, P. / Chitnumsub, P. / Maenpuen, S.
Funding support Thailand, 2items
OrganizationGrant numberCountry
National Center for Genetic Engineering and Biotechnology (Thailand)P16-52034 Thailand
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Catalytic and structural insights into a stereospecific and thermostable Class II aldolase HpaI from Acinetobacter baumannii.
Authors: Watthaisong, P. / Binlaeh, A. / Jaruwat, A. / Lawan, N. / Tantipisit, J. / Jaroensuk, J. / Chuaboon, L. / Phonbuppha, J. / Tinikul, R. / Chaiyen, P. / Chitnumsub, P. / Maenpuen, S.
History
DepositionMay 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxy-2-oxoheptanedioate aldolase
B: 4-hydroxy-2-oxoheptanedioate aldolase
C: 4-hydroxy-2-oxoheptanedioate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,85810
Polymers86,2683
Non-polymers5917
Water6,702372
1
A: 4-hydroxy-2-oxoheptanedioate aldolase
B: 4-hydroxy-2-oxoheptanedioate aldolase
C: 4-hydroxy-2-oxoheptanedioate aldolase
hetero molecules

A: 4-hydroxy-2-oxoheptanedioate aldolase
B: 4-hydroxy-2-oxoheptanedioate aldolase
C: 4-hydroxy-2-oxoheptanedioate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,71720
Polymers172,5356
Non-polymers1,18114
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area26960 Å2
ΔGint-393 kcal/mol
Surface area48780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.361, 90.311, 86.395
Angle α, β, γ (deg.)90.000, 122.200, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein 4-hydroxy-2-oxoheptanedioate aldolase


Mass: 28755.910 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: hpaI, FD887_17235 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A5R9HKL3, 4-hydroxy-2-oxoheptanedioate aldolase

-
Non-polymers , 5 types, 379 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-JBU / (4R,5R)-4,5,6-tris(oxidanyl)-2-oxidanylidene-hexanoic acid


Mass: 178.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 4.6 / Details: CaCl2, MPD, Na acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→24.38 Å / Num. obs: 88479 / % possible obs: 99.2 % / Redundancy: 4.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.061 / Rrim(I) all: 0.137 / Net I/σ(I): 8.7 / Num. measured all: 416803 / Scaling rejects: 841
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.833.11.8211341943170.4861.1432.1640.795.7
9.67-24.386.20.03930014830.9980.0160.04328.980.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PROTEUM PLUSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ET8

7et8


Resolution: 1.95→24.38 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.584 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 3195 4.9 %RANDOM
Rwork0.1849 ---
obs0.1866 62173 93.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.57 Å2 / Biso mean: 14.19 Å2 / Biso min: 5.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å20.15 Å2
2---0.12 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.95→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 28 372 6181
Biso mean--24.51 17.72 -
Num. residues----759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135905
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175661
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6167979
X-RAY DIFFRACTIONr_angle_other_deg1.3751.57513141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21924.338272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.412151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0381524
X-RAY DIFFRACTIONr_chiral_restr0.0750.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 229 -
Rwork0.268 4599 -
all-4828 -
obs--94.09 %

+
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