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- PDB-4k3v: Structure of Staphylococcus aureus MntC -

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Basic information

Entry
Database: PDB / ID: 4k3v
TitleStructure of Staphylococcus aureus MntC
ComponentsABC superfamily ATP binding cassette transporter, binding protein
KeywordsTRANSPORT PROTEIN / Mn2+ specific mntABC transporter
Function / homologyNitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsParris, K.D. / Mosyak, L.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Three-Dimensional Structure and Biophysical Characterization of Staphylococcus aureus Cell Surface Antigen-Manganese Transporter MntC.
Authors: Gribenko, A. / Mosyak, L. / Ghosh, S. / Parris, K. / Svenson, K. / Moran, J. / Chu, L. / Li, S. / Liu, T. / Woods, V.L. / Jansen, K.U. / Green, B.A. / Anderson, A.S. / Matsuka, Y.V.
History
DepositionApr 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_label_asym_id / _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: ABC superfamily ATP binding cassette transporter, binding protein
B: ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7034
Polymers69,5932
Non-polymers1102
Water2,774154
1
A: ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8522
Polymers34,7971
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8522
Polymers34,7971
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.480, 68.360, 107.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC superfamily ATP binding cassette transporter, binding protein


Mass: 34796.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: JKD6159 / Gene: mntC, SAA6159_00586 / Production host: Escherichia coli (E. coli) / References: UniProt: D9RF12
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Protein: 5.4 mg/ml, 150 mM sodium chloride, 25 mM tris hydrochloride, pH 8.0 Well: 34% Jeffamine ED-2001, 100 mM HEPES, pH 7.8 at 18C., VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→23 Å / Num. all: 26334 / Num. obs: 24405 / % possible obs: 92.7 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Biso Wilson estimate: 26.39 Å2
Reflection shellResolution: 2.2→2.24 Å / % possible all: 88.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
BUSTER2.11.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HH8

3hh8


Resolution: 2.2→23 Å / Cor.coef. Fo:Fc: 0.9108 / Cor.coef. Fo:Fc free: 0.8959 / SU R Cruickshank DPI: 0.578 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1039 5.06 %RANDOM
Rwork0.1979 ---
obs0.199 20528 79.03 %-
all-24405 --
Displacement parametersBiso mean: 40.32 Å2
Baniso -1Baniso -2Baniso -3
1-8.6809 Å20 Å20 Å2
2--7.3512 Å20 Å2
3----16.032 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 2.2→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 2 154 4404
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094325HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.185807HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1588SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes136HARMONIC2
X-RAY DIFFRACTIONt_gen_planes590HARMONIC5
X-RAY DIFFRACTIONt_it4325HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion18.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion559SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4990SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.32 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2543 122 4.94 %
Rwork0.2004 2346 -
all0.2029 2468 -
obs--79.03 %

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