[English] 日本語
Yorodumi
- PDB-4l7z: Crystal Structure of Chloroflexus aurantiacus malyl-CoA lyase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l7z
TitleCrystal Structure of Chloroflexus aurantiacus malyl-CoA lyase
ComponentsHpcH/HpaI aldolase
KeywordsLYASE / TIM barrel
Function / homology
Function and homology information


malyl-CoA lyase / carbon fixation by 3-hydroxypropionate cycle / L-erythro-3-methylmalyl-CoA lyase activity / malyl-CoA lyase activity / (S)-citramalyl-CoA lyase / (S)-citramalyl-CoA lyase activity / oxaloacetate metabolic process / magnesium ion binding / metal ion binding
Similarity search - Function
Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / 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
Malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase / Malyl-CoA/beta-methylmalyl-CoA/citramalyl-CoA lyase
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.502 Å
AuthorsZarzycki, J. / Kerfeld, C.A.
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases.
Authors: Zarzycki, J. / Kerfeld, C.A.
History
DepositionJun 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HpcH/HpaI aldolase
B: HpcH/HpaI aldolase
C: HpcH/HpaI aldolase
D: HpcH/HpaI aldolase
E: HpcH/HpaI aldolase
F: HpcH/HpaI aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,7368
Polymers230,4926
Non-polymers2442
Water17,745985
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29790 Å2
ΔGint-140 kcal/mol
Surface area70140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.552, 157.815, 168.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-467-

HOH

-
Components

#1: Protein
HpcH/HpaI aldolase / malyl-CoA lyase


Mass: 38415.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: OK-70-fl / Gene: Caur_0174, mcl / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A9WC35, UniProt: S5N020*PLUS, malyl-CoA lyase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 985 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 1 part protein solution (3.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 1 part buffer (60 mM Bis-Tris propane/citric acid, pH 6.6, 20% w/v PEG3350, ...Details: 1 part protein solution (3.5 mg/mL in 20 mM Tris-HCl, pH 7.5, 2 mM magnesium chloride, 100 mM sodium chloride) + 1 part buffer (60 mM Bis-Tris propane/citric acid, pH 6.6, 20% w/v PEG3350, 20 mM magnesium chloride), VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2011
RadiationMonochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.502→38.535 Å / Num. all: 88943 / Num. obs: 88943 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rsym value: 0.155 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.502-2.645.40.6851.167153125260.68597.3
2.64-2.86.70.6061.281444122030.606100
2.8-2.996.70.4141.876646115110.414100
2.99-3.236.80.2822.772678107230.282100
3.23-3.546.80.1946738698760.19100
3.54-3.966.70.12666067689930.126100
3.96-4.576.70.0819.25295979630.081100
4.57-5.596.60.06710.74491367820.067100
5.59-7.916.50.06211.63461653220.062100
7.91-38.5356.40.03815.61954430440.03899.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å38.54 Å
Translation3 Å38.54 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
PHENIX1.8.2_1303refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L9Y

4l9y


Resolution: 2.502→38.535 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 0.8 / Phase error: 27.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1992 2.26 %
Rwork0.1904 --
obs0.1914 88820 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.76 Å2 / Biso mean: 21.7119 Å2 / Biso min: 4.55 Å2
Refinement stepCycle: LAST / Resolution: 2.502→38.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15960 0 16 985 16961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216370
X-RAY DIFFRACTIONf_angle_d0.59722239
X-RAY DIFFRACTIONf_chiral_restr0.0412444
X-RAY DIFFRACTIONf_plane_restr0.0032911
X-RAY DIFFRACTIONf_dihedral_angle_d11.3926047
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.502-2.53330.49861140.37165231534584
2.5333-2.56660.37451130.31536074618798
2.5666-2.60170.28341610.268161876348100
2.6017-2.63890.32341550.26261876342100
2.6389-2.67830.35381610.25362396400100
2.6783-2.72010.28891290.248461896318100
2.7201-2.76470.29551220.251762266348100
2.7647-2.81240.32181900.261461066296100
2.8124-2.86350.331260.25161826308100
2.8635-2.91860.26911410.231762266367100
2.9186-2.97810.32041410.229162126353100
2.9781-3.04280.29731620.224862156377100
3.0428-3.11360.32171230.220462046327100
3.1136-3.19140.28861380.216261626300100
3.1914-3.27770.27861670.201361816348100
3.2777-3.37410.26291250.212662076332100
3.3741-3.48290.23781510.201561776328100
3.4829-3.60730.24571410.192562326373100
3.6073-3.75160.21191500.169661716321100
3.7516-3.92220.22141400.164862276367100
3.9222-4.12870.20881410.156862216362100
4.1287-4.38710.16931430.140561996342100
4.3871-4.72530.15041290.131561806309100
4.7253-5.19980.15851490.134661996348100
5.1998-5.94980.20981440.150362046348100
5.9498-7.48710.19851470.168361826329100
7.4871-38.540.13911460.140361896335100

+
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