[English] 日本語
Yorodumi
- PDB-8vab: Crystal structure of FeII/FeII CtCADD from Chlamydia trachomatis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vab
TitleCrystal structure of FeII/FeII CtCADD from Chlamydia trachomatis
Components4-aminobenzoate synthase
KeywordsOXIDOREDUCTASE / FeII reconstituted form
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / small molecule metabolic process / sulfur compound metabolic process / toxin activity / host cell cytoplasm / oxidoreductase activity / extracellular region / metal ion binding
Similarity search - Function
Putative folate metabolism protein, CADD family / Iron-containing redox enzyme / Pyrroloquinoline-quinone synthase-like / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Haem oxygenase-like, multi-helical
Similarity search - Domain/homology
: / 4-aminobenzoate synthase
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPhan, H.N. / Swartz, P.D. / Makris, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135315 United States
CitationJournal: Biochemistry / Year: 2024
Title: Assembly of a Heterobimetallic Fe/Mn Cofactor in the para -Aminobenzoate Synthase Chlamydia Protein Associating with Death Domains (CADD) Initiates Long-Range Radical Hole-Hopping.
Authors: Phan, H.N. / Swartz, P.D. / Gangopadhyay, M. / Guo, Y. / Smirnov, A.I. / Makris, T.M.
History
DepositionDec 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-aminobenzoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8813
Polymers27,7691
Non-polymers1122
Water57632
1
A: 4-aminobenzoate synthase
hetero molecules

A: 4-aminobenzoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7626
Polymers55,5392
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area2400 Å2
ΔGint-65 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.882, 92.882, 122.743
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

-
Components

#1: Protein 4-aminobenzoate synthase


Mass: 27769.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: Strain D/UW-3/Cx / Gene: CT_610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O84616
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.3 % / Description: Hexagonal plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M Lithium citrate tribasic tetrahydrate, 20% w/v PEG-3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 18, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.65→18.11 Å / Num. obs: 9563 / % possible obs: 98.04 % / Redundancy: 18.2 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2071 / Rpim(I) all: 0.04942 / Rrim(I) all: 0.213 / Net I/σ(I): 8.77
Reflection shellResolution: 2.65→2.744 Å / Rmerge(I) obs: 1.008 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.912 / CC star: 0.977 / Rpim(I) all: 0.2437 / Rrim(I) all: 1.038 / % possible all: 95.61

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisPro42.90adata reduction
Aimless1.12.15data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→18.11 Å / SU ML: 0.425 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3205
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2749 943 10.01 %
Rwork0.2039 8482 -
obs0.2107 9425 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.6 Å2
Refinement stepCycle: LAST / Resolution: 2.65→18.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 2 32 1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751694
X-RAY DIFFRACTIONf_angle_d0.88072299
X-RAY DIFFRACTIONf_chiral_restr0.0476247
X-RAY DIFFRACTIONf_plane_restr0.0067298
X-RAY DIFFRACTIONf_dihedral_angle_d5.2465231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.790.45461270.29061151X-RAY DIFFRACTION96.45
2.79-2.960.35591300.28441162X-RAY DIFFRACTION97.29
2.96-3.190.33681320.27471185X-RAY DIFFRACTION98.36
3.19-3.510.35251330.22361200X-RAY DIFFRACTION99.26
3.51-4.010.25721350.1841208X-RAY DIFFRACTION98.97
4.01-5.040.21241380.1651242X-RAY DIFFRACTION99.57
5.04-18.110.23351480.18581334X-RAY DIFFRACTION99.8

+
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