[English] 日本語
Yorodumi
- PDB-4jb7: 1.42 Angstrom resolution crystal structure of accessory colonizat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jb7
Title1.42 Angstrom resolution crystal structure of accessory colonization factor AcfC (acfC) in complex with D-aspartic acid
ComponentsAccessory colonization factor AcfC
KeywordsCELL INVASION / Accessory colonization factor AcfC / Virulence / Pathogenesis / CSGID / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / alpha/beta fold / Cellular processes
Function / homology
Function and homology information


sulfur compound metabolic process / sulfate transmembrane transport / sulfate binding / outer membrane-bounded periplasmic space / extracellular space
Similarity search - Function
Thiosulphate/Sulfate-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MALATE / TRIETHYLENE GLYCOL / Accessory colonization factor AcfC
Similarity search - Component
Biological speciesVibrio cholerae O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.42 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Dubrovska, I. / Winsor, J. / Minasov, G. / Shuvalova, L. / Filippova, E.V. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.42 Angstrom resolution crystal structure of accessory colonization factor AcfC (acfC) in complex with D-aspartic acid
Authors: Halavaty, A.S. / Wawrzak, Z. / Dubrovska, I. / Winsor, J. / Minasov, G. / Shuvalova, L. / Filippova, E.V. / Peterson, S.N. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Accessory colonization factor AcfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3785
Polymers28,8211
Non-polymers5574
Water6,575365
1
A: Accessory colonization factor AcfC
hetero molecules

A: Accessory colonization factor AcfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,75610
Polymers57,6432
Non-polymers1,1138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5370 Å2
ΔGint7 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.343, 72.343, 87.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Accessory colonization factor AcfC


Mass: 28821.480 Da / Num. of mol.: 1 / Fragment: accessory colonization factor AcfC
Mutation: 24 N-terminal residues were truncated to produce the construct with residues 25 through 256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: acfC, VC_0841 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q9KTQ6
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein: 7.3 mg/mL in 10 mM Tris-HCl, pH 8.0, 0.25 M NaCl 5 mM BME. Crystallization: PACT Suite D6(#42): 0.1 M MMT buffer pH 9.0 25 % (w/v) PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
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: Feb 13, 2013 / Details: Be-Lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.42→30 Å / Num. all: 44772 / Num. obs: 44772 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 45.47
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3.82 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
MLPHAREphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.42→27.93 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.501 / SU ML: 0.028 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14148 2249 5 %RANDOM
Rwork0.12589 ---
obs0.12667 42343 99.95 %-
all-42343 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.643 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20 Å2
2---0.03 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.42→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 37 365 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222037
X-RAY DIFFRACTIONr_bond_other_d0.0010.021390
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9452768
X-RAY DIFFRACTIONr_angle_other_deg0.9433398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6465260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76224.68194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.72115338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.747159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02422
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_it1.0361.51245
X-RAY DIFFRACTIONr_mcbond_other0.371.5501
X-RAY DIFFRACTIONr_mcangle_it1.70522018
X-RAY DIFFRACTIONr_scbond_it2.6353792
X-RAY DIFFRACTIONr_scangle_it4.064.5750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.169 149 -
Rwork0.159 3051 -
obs--100 %
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)
11.2620.2155-0.1131.49280.08660.84910.0929-0.2163-0.03410.2991-0.0897-0.15320.01780.1081-0.00320.0868-0.0249-0.04290.04980.00960.02822.496714.610222.7959
21.74990.12831.0191.4095-0.55251.986-0.05670.07110.0489-0.005-0.0503-0.2104-0.05890.36940.10710.0118-0.0063-0.00350.08890.00670.049925.415412.94347.7511
30.7735-0.00390.30960.4748-0.04480.9365-0.0016-0.03520.03440.0253-0.00370.0448-0.0411-0.08420.00530.00450.00440.00320.0089-0.00150.01243.183515.78154.2265
48.6005-0.05662.38644.24410.22174.3036-0.128-0.31580.52380.1742-0.05460.1026-0.3531-0.16880.18260.07870.03450.00620.0555-0.04770.08410.40528.369313.1769
50.8705-0.18840.07030.8175-0.11190.6896-0.0143-0.1218-0.00540.09240.01180.09910.002-0.14360.00250.04020.00130.00790.0458-0.00130.03013.693311.525611.9963
62.76960.55090.32351.2381-0.22411.50630.1999-0.1356-0.27060.2129-0.1462-0.13910.11020.0919-0.05370.0942-0.0141-0.04010.0350.03270.051818.85552.801122.1387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 76
2X-RAY DIFFRACTION2A77 - 92
3X-RAY DIFFRACTION3A93 - 178
4X-RAY DIFFRACTION4A179 - 187
5X-RAY DIFFRACTION5A188 - 225
6X-RAY DIFFRACTION6A226 - 256

+
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