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- PDB-4m58: Crystal Structure of an transition metal transporter -

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Basic information

Entry
Database: PDB / ID: 4m58
TitleCrystal Structure of an transition metal transporter
ComponentsCobalamin biosynthesis protein CbiM
KeywordsMEMBRANE PROTEIN / transporter / Nickel
Function / homology
Function and homology information


transition metal ion transport / plasma membrane
Similarity search - Function
Metal transport protein CbiM/NikMN / Cobalt uptake substrate-specific transmembrane region / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Cobalamin biosynthesis protein CbiM
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.21 Å
AuthorsYu, Y. / Yan, C.Y. / Zhang, B. / Li, X.L. / Gu, J.K.
CitationJournal: Cell Res. / Year: 2014
Title: Planar substrate-binding site dictates the specificity of ECF-type nickel/cobalt transporters
Authors: Yu, Y. / Zhou, M.Z. / Kirsch, F. / Xu, C.Q. / Zhang, L. / Wang, Y. / Jiang, Z. / Wang, N. / Li, J. / Eitinger, T. / Yang, M.J.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cobalamin biosynthesis protein CbiM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4312
Polymers25,3721
Non-polymers591
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.727, 122.727, 125.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Cobalamin biosynthesis protein CbiM / / TtNikM2


Mass: 25371.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Gene: CbiM2, TTE1695 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R9C0
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.37 Å3/Da / Density % sol: 77.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 38% PEG 300, 0.05M Glycine, 0.1M sodium chloride, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→30.06 Å / Num. all: 9615 / Num. obs: 9403 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 3.2 Å

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.21→30.056 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6662 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 37.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2874 450 4.8 %RANDOM
Rwork0.2451 ---
all0.247 9615 --
obs0.247 9368 97.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245.29 Å2 / Biso mean: 117.8871 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.21→30.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 1 0 1680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141718
X-RAY DIFFRACTIONf_angle_d2.0122342
X-RAY DIFFRACTIONf_dihedral_angle_d14.371591
X-RAY DIFFRACTIONf_chiral_restr0.106283
X-RAY DIFFRACTIONf_plane_restr0.011290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2096-3.67340.33371470.2661293099
3.6734-4.62540.23721370.2555297299
4.6254-30.05730.29751660.2361301695
Refinement TLS params.Method: refined / Origin x: 17.4198 Å / Origin y: 55.1824 Å / Origin z: 59.3665 Å
111213212223313233
T0.4799 Å20.2642 Å2-0.1265 Å2-1.9302 Å2-0.0737 Å2--0.7996 Å2
L3.8105 °2-0.7944 °20.5764 °2-2.5909 °2-1.0042 °2--1.9583 °2
S0.2641 Å °0.8993 Å °-0.3276 Å °-0.5298 Å °-0.0057 Å °0.1459 Å °-0.5419 Å °-0.4138 Å °-0.0899 Å °
Refinement TLS groupSelection details: chain A

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