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- PDB-5m95: STAPHYLOCOCCUS CAPITIS DIVALENT METAL ION TRANSPORTER (DMT) IN CO... -

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Basic information

Entry
Database: PDB / ID: 5m95
TitleSTAPHYLOCOCCUS CAPITIS DIVALENT METAL ION TRANSPORTER (DMT) IN COMPLEX WITH MANGANESE
Components
  • CAMELID ANTIBODY FRAGMENT, NANOBODY
  • Divalent metal cation transporter MntH
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / TRANSPORTER / SLC11 / TRANSITION METAL IONS / NRAMP / DMT / LEUT FOLD
Function / homology
Function and homology information


metal ion transmembrane transporter activity / symporter activity / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
NRAMP family / Natural resistance-associated macrophage protein-like / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Divalent metal cation transporter MntH
Similarity search - Component
Biological speciesStaphylococcus capitis (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsEhrnstorfer, I.A. / Geertsma, E.R. / Pardon, E. / Steyaert, J. / Dutzler, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Crystal Structure Of A Slc11 (Nramp) Transporter Reveals The Basis For Transition-Metal Ion Transport.
Authors: Ehrnstorfer, I.A. / Geertsma, E.R. / Pardon, E. / Steyaert, J. / Dutzler, R.
History
DepositionOct 31, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionNov 30, 2016ID: 4WGW
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.2Sep 25, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Divalent metal cation transporter MntH
B: CAMELID ANTIBODY FRAGMENT, NANOBODY
D: CAMELID ANTIBODY FRAGMENT, NANOBODY
C: Divalent metal cation transporter MntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2086
Polymers118,0984
Non-polymers1102
Water00
1
A: Divalent metal cation transporter MntH
B: CAMELID ANTIBODY FRAGMENT, NANOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1043
Polymers59,0492
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: CAMELID ANTIBODY FRAGMENT, NANOBODY
C: Divalent metal cation transporter MntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1043
Polymers59,0492
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.170, 114.170, 257.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND SEGID A
211CHAIN C AND SEGID A
112CHAIN B AND SEGID B
212CHAIN D AND SEGID B

NCS ensembles :
ID
1
2

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Components

#1: Protein Divalent metal cation transporter MntH


Mass: 45521.875 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 43-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus capitis (bacteria)
Gene: mntH, BN1317_80025, SCAPIOD100025, SCAPIOD110024, SCAPIOD130025
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4MEX1
#2: Antibody CAMELID ANTIBODY FRAGMENT, NANOBODY


Mass: 13526.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
Has protein modificationY

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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: 4.3 Å3/Da / Density % sol: 71.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 24 % PEG 400, 200 MM CACL2, 50 MM HEPES, PH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.894 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.894 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 27350 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 137.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 19
Reflection shellResolution: 3.4→3.6 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIXdev_1760refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WGV

4wgv
PDB Unreleased entry


Resolution: 3.4→19.9 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 28.37
RfactorNum. reflection% reflection
Rfree0.292 1336 4.88 %
Rwork0.252 --
obs0.253 27350 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 152.5 Å2
Refinement stepCycle: LAST / Resolution: 3.4→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7946 0 2 0 7948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038102
X-RAY DIFFRACTIONf_angle_d0.69411014
X-RAY DIFFRACTIONf_dihedral_angle_d12.3372876
X-RAY DIFFRACTIONf_chiral_restr0.0261338
X-RAY DIFFRACTIONf_plane_restr0.0031364
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A3522X-RAY DIFFRACTIONPOSITIONAL
12C3522X-RAY DIFFRACTIONPOSITIONAL
21B1122X-RAY DIFFRACTIONPOSITIONAL
22D1122X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.5210.2821410.29582542X-RAY DIFFRACTION100
3.521-3.66110.33591290.29992568X-RAY DIFFRACTION100
3.6611-3.82670.33391380.28932551X-RAY DIFFRACTION100
3.8267-4.02680.29541350.25722567X-RAY DIFFRACTION100
4.0268-4.27680.25511170.23082564X-RAY DIFFRACTION100
4.2768-4.60320.27661240.22262615X-RAY DIFFRACTION100
4.6032-5.05960.25931570.22182562X-RAY DIFFRACTION100
5.0596-5.7760.28531510.25472599X-RAY DIFFRACTION100
5.776-7.21890.30471100.29472684X-RAY DIFFRACTION100
7.2189-19.90090.30471340.24232762X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.1586 Å / Origin y: 114.0283 Å / Origin z: -13.1885 Å
111213212223313233
T0.683 Å20.1002 Å2-0.0358 Å2-0.7465 Å2-0.1164 Å2--0.7325 Å2
L3.2776 °2-0.5461 °2-0.6045 °2-1.5137 °20.0641 °2--0.9419 °2
S0.1583 Å °0.601 Å °-0.0269 Å °-0.053 Å °-0.0725 Å °0.057 Å °-0.1035 Å °-0.1996 Å °-0.0025 Å °
Refinement TLS groupSelection details: ALL

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