[English] 日本語
Yorodumi
- PDB-3c9h: Crystal structure of the substrate binding protein of the ABC tra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c9h
TitleCrystal structure of the substrate binding protein of the ABC transporter from Agrobacterium tumefaciens
ComponentsABC transporter, substrate binding protein
KeywordsTRANSPORT PROTEIN / substrate binding protein / ABC transporter / Structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-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
CITRIC ACID / ABC transporter, substrate binding protein (Iron)
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the substrate binding protein of the ABC transporter from Agrobacterium tumefaciens.
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: ABC transporter, substrate binding protein
B: ABC transporter, substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3636
Polymers78,9302
Non-polymers4334
Water7,800433
1
A: ABC transporter, substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6813
Polymers39,4651
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter, substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6813
Polymers39,4651
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.313, 86.947, 109.642
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ABC transporter, substrate binding protein


Mass: 39465.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: GI:17936349, AGR_C_4480, Atu2467 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7CWZ6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium citrate, 0.2M Ammonium acetate, 30% PEG 4000, 10mM ATP, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2006 / Details: Mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→68.2 Å / Num. all: 54496 / Num. obs: 54136 / % possible obs: 99.34 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 19.78
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 1.57 / Num. unique all: 4178 / % possible all: 97.77

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→35.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.333 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.497 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22817 2898 5.1 %RANDOM
Rwork0.17259 ---
all0.17539 54136 --
obs0.17539 54136 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2--1.49 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5265 0 28 433 5726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225415
X-RAY DIFFRACTIONr_bond_other_d0.0010.023672
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9567356
X-RAY DIFFRACTIONr_angle_other_deg0.93438897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94623.306245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92115871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9771542
X-RAY DIFFRACTIONr_chiral_restr0.0840.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021136
X-RAY DIFFRACTIONr_nbd_refined0.2180.21185
X-RAY DIFFRACTIONr_nbd_other0.1980.23819
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22594
X-RAY DIFFRACTIONr_nbtor_other0.0860.22743
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2376
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.219
X-RAY DIFFRACTIONr_mcbond_it1.4861.54314
X-RAY DIFFRACTIONr_mcbond_other0.5441.51351
X-RAY DIFFRACTIONr_mcangle_it1.72625399
X-RAY DIFFRACTIONr_scbond_it3.03332439
X-RAY DIFFRACTIONr_scangle_it4.114.51957
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 206 -
Rwork0.235 3879 -
obs-4085 97.77 %
Refinement TLS params.Method: refined / Origin x: 37.753 Å / Origin y: -0.084 Å / Origin z: 11.145 Å
111213212223313233
T-0.0293 Å20.0063 Å2-0.0003 Å2--0.0228 Å20.0024 Å2---0.0462 Å2
L0.6245 °20.1767 °2-0.0115 °2-0.1016 °2-0.0221 °2--0.2935 °2
S0.0131 Å °0.0196 Å °0.0044 Å °-0.0151 Å °0.0184 Å °-0.0024 Å °-0.0121 Å °-0.0162 Å °-0.0314 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA16 - 6016 - 60
2X-RAY DIFFRACTION1AA61 - 10061 - 100
3X-RAY DIFFRACTION1AA101 - 150101 - 150
4X-RAY DIFFRACTION1AA151 - 200151 - 200
5X-RAY DIFFRACTION1AA201 - 250201 - 250
6X-RAY DIFFRACTION1AA251 - 300251 - 300
7X-RAY DIFFRACTION1AA301 - 354301 - 354
8X-RAY DIFFRACTION1BB15 - 6015 - 60
9X-RAY DIFFRACTION1BB61 - 10061 - 100
10X-RAY DIFFRACTION1BB101 - 150101 - 150
11X-RAY DIFFRACTION1BB151 - 200151 - 200
12X-RAY DIFFRACTION1BB201 - 250201 - 250
13X-RAY DIFFRACTION1BB251 - 300251 - 300
14X-RAY DIFFRACTION1BB301 - 353301 - 353

+
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