[English] 日本語
Yorodumi
- PDB-2nzh: Crystal structure of a secretion chaperone CsaA from Bacillus sub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nzh
TitleCrystal structure of a secretion chaperone CsaA from Bacillus subtilis in the space group P 4 21 2
ComponentsProtein csaA
KeywordsCHAPERONE / Beta barrel / oligonucleotide/oligosaccharide binding fold / homodimer
Function / homology
Function and homology information


protein transport / tRNA binding / cytoplasm
Similarity search - Function
Probable chaperone CsaA / : / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Probable chaperone CsaA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShapova, Y.A. / Paetzel, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Crystallographic analysis of Bacillus subtilis CsaA.
Authors: Shapova, Y.A. / Paetzel, M.
History
DepositionNov 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_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_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: Protein csaA
B: Protein csaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4983
Polymers24,4062
Non-polymers921
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-20 kcal/mol
Surface area10560 Å2
MethodPISA
2
A: Protein csaA
B: Protein csaA
hetero molecules

A: Protein csaA
B: Protein csaA
hetero molecules

A: Protein csaA
B: Protein csaA
hetero molecules

A: Protein csaA
B: Protein csaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,99412
Polymers97,6258
Non-polymers3684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area19970 Å2
ΔGint-81 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.146, 109.146, 37.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-132-

HOH

-
Components

#1: Protein Protein csaA / Secretion chaperone CsaA


Mass: 12203.147 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: csaA, BSU19040 / Plasmid: BsCsaA/pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37584
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 30% PEG8000, 0.2M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 102 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 29, 2006 / Details: VariMax Cu HF
RadiationMonochromator: nickel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→54.57 Å / Num. obs: 17190 / % possible obs: 93.3 % / Observed criterion σ(I): 5 / Redundancy: 11.11 % / Rmerge(I) obs: 0.051 / Χ2: 0.99 / Net I/σ(I): 31.9 / Scaling rejects: 1444
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.99 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 7.2 / Num. measured all: 1383 / Num. unique all: 1578 / Χ2: 0.86 / % possible all: 87

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å54.57 Å
Translation3 Å54.57 Å

-
Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GD7

1gd7


Resolution: 1.9→54.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.721 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 885 5.2 %RANDOM
Rwork0.2 ---
all0.202 17165 --
obs0.202 17165 93.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.294 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.9→54.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 6 117 1777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221687
X-RAY DIFFRACTIONr_angle_refined_deg1.6062.0032287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99825.31264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72715299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.924159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021247
X-RAY DIFFRACTIONr_nbd_refined0.2030.2721
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2117
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.210
X-RAY DIFFRACTIONr_mcbond_it0.8361.51118
X-RAY DIFFRACTIONr_mcangle_it1.26721774
X-RAY DIFFRACTIONr_scbond_it2.2523618
X-RAY DIFFRACTIONr_scangle_it3.6734.5513
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 68 -
Rwork0.256 1091 -
obs-1159 85.85 %
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)
13.5285-0.4389-0.74391.18020.03862.1219-0.0156-0.03010.3035-0.0771-0.0211-0.1191-0.05810.17550.03670.0825-0.0434-0.02080.02290.01120.113644.4612-16.7038-1.6739
23.0988-0.36490.853.6535-0.19231.6008-0.08560.00180.2371-0.04090.0257-0.0444-0.0809-0.04760.05990.072-0.01760.01030.0634-0.01020.087231.2676-13.25671.7529
33.9785-0.11970.29841.48980.60960.27980.0856-0.00960.3311-0.0629-0.012-0.06940.0233-0.0141-0.07360.0797-0.0212-0.01180.06160.00760.092638.6944-16.521.9044
47.5019-3.67314.21016.6542-1.62372.4021-0.05350.11010.4114-0.0383-0.1786-0.3207-0.11940.02020.23210.034-0.02190.00350.01380.0010.127536.1818-4.20780.5134
52.1481-0.12220.81061.82570.13642.8670.10610.07250.099-0.0641-0.07770.01910.1173-0.1376-0.02840.0724-0.01840.0060.08370.00170.056837.7815-22.787-2.5304
62.43540.34860.96116.7911-0.03412.860.0178-0.05180.3919-0.1718-0.0067-0.0294-0.22750.1038-0.01120.0808-0.02710.02270.09110.01080.038644.4184-22.2744-12.9404
734.650525.38378.482319.7760.358131.1164-0.97270.5396-3.5635-0.50290.1666-1.9782-0.17751.55480.80610.11890.11960.00370.1158-0.0230.150254.3008-44.7884-9.6942
81.07730.67530.87742.0226-1.1673.99890.15760.01760.0051-0.2924-0.1699-0.22890.47540.37760.01230.16130.01630.01720.1121-0.00150.00146.9349-35.3617-15.0753
92.7103-1.57180.32651.7852-1.02743.92780.0475-0.1127-0.1407-0.06290.09090.0280.31110.1051-0.13840.1046-0.0259-0.0170.04270.02130.01246.2532-39.1046-6.263
100.9188-1.3476-0.16352.5751-1.04562.7890.17850.11270.1435-0.1822-0.0842-0.47590.22220.2439-0.09430.1091-0.01780.00050.0653-0.01930.046649.8625-29.2821-13.6515
111.315-0.4627-0.26862.45140.56425.25570.0063-0.08020.1423-0.14910.1078-0.44290.33820.4865-0.1140.05780.01140.00240.0797-0.00750.081450.5123-31.7928-6.0613
120.4519-0.9761-1.13973.51780.40315.88210.0684-0.0337-0.0306-0.0012-0.1104-0.12160.0838-0.32660.04210.0578-0.049-0.0150.10460.00460.013334.4965-26.1228-10.5424
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 224 - 25
22AA23 - 5826 - 61
33AA59 - 7262 - 75
44AA73 - 8276 - 85
55AA83 - 11086 - 113
66BB3 - 206 - 23
77BB21 - 2524 - 28
88BB26 - 4329 - 46
99BB44 - 6147 - 64
1010BB62 - 7565 - 78
1111BB76 - 9779 - 100
1212BB98 - 110101 - 113

+
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