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- PDB-4irm: Crystal structure of mntc r116a mutant exhibits flexibility in th... -

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Basic information

Entry
Database: PDB / ID: 4irm
TitleCrystal structure of mntc r116a mutant exhibits flexibility in the c-terminal domain
ComponentsMn transporter; MntC
KeywordsTRANSPORT PROTEIN / manganese / solute binding protein of ABS transporter
Function / homology
Function and homology information


metal ion transport / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Mn transporter MntC
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKanteev, M. / Adir, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Arginine 116 stabilizes the entrance to the metal ion-binding site of the MntC protein.
Authors: Kanteev, M. / Adir, N.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 6, 2013ID: 3V63
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Sep 20, 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 / 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_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_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Mn transporter; MntC
B: Mn transporter; MntC
C: Mn transporter; MntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2076
Polymers108,0423
Non-polymers1653
Water0
1
A: Mn transporter; MntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0692
Polymers36,0141
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mn transporter; MntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0692
Polymers36,0141
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mn transporter; MntC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0692
Polymers36,0141
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.400, 128.400, 90.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Mn transporter; MntC


Mass: 36014.133 Da / Num. of mol.: 3 / Mutation: R116A
Source method: isolated from a genetically manipulated source
Details: includes TEV cleavage site / Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: mntC / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q79EF9
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn

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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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 290 K / pH: 6.5
Details: PEG 4000, SODIUM CACODYLATE, 50mM ZINC CHLORIDE,, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.5→24.5 Å / Num. obs: 11028 / % possible obs: 99 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 15
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 6.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UJP

3ujp


Resolution: 3.5→24.5 Å / Isotropic thermal model: Isotropic / Phase error: 35.89 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.305 528 4.85 %
Rwork0.294 --
obs0.294 10882 97.9 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.19 Å2 / ksol: 0.24 e/Å3
Displacement parametersBiso mean: 97.5 Å2
Refinement stepCycle: LAST / Resolution: 3.5→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5879 0 3 0 5882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.056010
X-RAY DIFFRACTIONf_angle_d2.958210
X-RAY DIFFRACTIONf_dihedral_angle_d18.7332177
X-RAY DIFFRACTIONf_chiral_restr0.138935
X-RAY DIFFRACTIONf_plane_restr0.021071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5035-3.85430.53481180.50962472X-RAY DIFFRACTION91
3.8543-4.40790.30491330.31852599X-RAY DIFFRACTION95
4.4079-5.53790.28791260.26382632X-RAY DIFFRACTION95
5.5379-21.59750.261430.24982639X-RAY DIFFRACTION92

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