[English] 日本語
Yorodumi
- PDB-7f6k: Crystal structure of metal-citrate-binding protein (MctA) of ABC ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f6k
TitleCrystal structure of metal-citrate-binding protein (MctA) of ABC transporter endogenously bound to citrate
ComponentsIron ABC transporter, periplasmic iron-binding protein
KeywordsTRANSPORT PROTEIN / Substrate-binding protein / metal ion / secondary transporter / symporter
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACETATE ION / CITRIC ACID / CARBON DIOXIDE / Iron ABC transporter, periplasmic iron-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKanaujia, S.P. / Mandal, S.K. / Gogoi, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR16065/NER/95/61/2015 India
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural and thermodynamic insights into a novel Mg 2+ -citrate-binding protein from the ABC transporter superfamily.
Authors: Mandal, S.K. / Kanaujia, S.P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2021
Title: Structural and thermodynamic insights into a novel Mg2+-citrate-binding protein from the ABC transporter superfamily
Authors: Mandal, S.K. / Kanaujia, S.P.
History
DepositionJun 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron ABC transporter, periplasmic iron-binding protein
B: Iron ABC transporter, periplasmic iron-binding protein
C: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,25122
Polymers114,5503
Non-polymers1,70119
Water8,647480
1
A: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,91310
Polymers38,1831
Non-polymers7299
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9279
Polymers38,1831
Non-polymers7448
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4113
Polymers38,1831
Non-polymers2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.550, 145.110, 79.240
Angle α, β, γ (deg.)90.000, 100.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERVALVALAA3 - 3375 - 339
221SERSERVALVALBB3 - 3375 - 339
132ASPASPALAALAAA8 - 33610 - 338
242ASPASPALAALACC8 - 33610 - 338
153ASPASPALAALABB8 - 33610 - 338
263ASPASPALAALACC8 - 33610 - 338

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Iron ABC transporter, periplasmic iron-binding protein


Mass: 38183.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHB177 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53VZ2

-
Non-polymers , 9 types, 499 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.4 % / Description: Monoclinic
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 0.2 M ammonium sulphate, 0.1 M MES mohohydrate pH 6.5, 30% (w/v) PEG monoethyl ether 5000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 2017 / Details: VariMax HF
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→77.93 Å / Num. obs: 58898 / % possible obs: 100 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.063 / Rrim(I) all: 0.122 / Net I/σ(I): 9.2 / Num. measured all: 213306 / Scaling rejects: 27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.163.40.4391575545700.8330.2780.5222.899.7
9.15-77.933.60.03926307370.9970.0240.0462299.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.08 Å72.55 Å

-
Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.3.0data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.9.4.1model building
REFMAC5.8.0267refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F6E

7f6e


Resolution: 2.1→72.66 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.485 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2893 4.9 %RANDOM
Rwork0.1693 ---
obs0.1715 55970 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.06 Å2 / Biso mean: 41.639 Å2 / Biso min: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å20.96 Å2
2--0.15 Å20 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 2.1→72.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7902 0 102 480 8484
Biso mean--41.72 34.2 -
Num. residues----1003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0138243
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177893
X-RAY DIFFRACTIONr_angle_refined_deg1.681.64911191
X-RAY DIFFRACTIONr_angle_other_deg1.4081.57618085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.71351024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93920.588459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.259151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1221578
X-RAY DIFFRACTIONr_chiral_restr0.0780.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022039
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A111660.07
12B111660.07
21A108020.09
22C108020.09
31B108680.08
32C108680.08
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 224 -
Rwork0.226 4120 -
all-4344 -
obs--99.68 %
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)
10.8018-0.33340.220.6041-0.27691.0153-0.01560.1043-0.0317-0.0346-0.0358-0.02790.10070.01970.05150.0388-0.00850.03720.079-0.00540.03911.298912.732110.7411
20.83420.1167-0.2130.86920.12440.5298-0.0685-0.14050.07560.05210.04770.04560.03-0.01130.02090.01650.02960.00080.0983-0.01740.01791.141530.339943.1179
32.7664-0.3204-1.06732.38761.20412.9066-0.6245-0.1995-0.63960.11590.0458-0.180.93830.20170.57880.49890.1320.30290.12860.10530.313421.677859.62898.1116
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 338
2X-RAY DIFFRACTION2B3 - 339
3X-RAY DIFFRACTION3C8 - 337

+
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