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- PDB-4nno: Crystal Structure of Manganese ABC transporter substrate-binding ... -

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Basic information

Entry
Database: PDB / ID: 4nno
TitleCrystal Structure of Manganese ABC transporter substrate-binding protein MntC from Staphylococcus Aureus bound to a Zinc ion
ComponentsLipoprotein
KeywordsTRANSPORT PROTEIN / Manganese transporter / MRSA / ABC superfamily ATP binding cassette 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipoprotein / Lipoprotein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.174 Å
AuthorsRouge, L. / Ahuja, S. / Sudhamsu, J.
CitationJournal: Structure / Year: 2015
Title: Structural analysis of bacterial ABC transporter inhibition by an antibody fragment.
Authors: Ahuja, S. / Rouge, L. / Swem, D.L. / Sudhamsu, J. / Wu, P. / Russell, S.J. / Alexander, M.K. / Tam, C. / Nishiyama, M. / Starovasnik, M.A. / Koth, C.M.
History
DepositionNov 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Sep 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_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_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: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9562
Polymers32,8901
Non-polymers651
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.570, 63.440, 69.600
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 Lipoprotein


Mass: 32890.176 Da / Num. of mol.: 1 / Fragment: UNP residues 19-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: SAV0631 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99VY4, UniProt: A0A0H3JTS7*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2012
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.17→35.56 Å / Num. all: 80500 / Num. obs: 80500 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 %

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSZ

1psz


Resolution: 1.174→35.56 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 14.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1602 2000 2.48 %Random
Rwork0.1506 ---
obs0.1509 80500 99.06 %-
all-80500 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.174→35.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 1 297 2517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092356
X-RAY DIFFRACTIONf_angle_d1.0893188
X-RAY DIFFRACTIONf_dihedral_angle_d11.734934
X-RAY DIFFRACTIONf_chiral_restr0.076344
X-RAY DIFFRACTIONf_plane_restr0.005410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.174-1.20340.19281410.15035544X-RAY DIFFRACTION99
1.2034-1.23590.14891420.14485541X-RAY DIFFRACTION99
1.2359-1.27230.16331400.145533X-RAY DIFFRACTION99
1.2723-1.31330.16521430.13255579X-RAY DIFFRACTION99
1.3133-1.36030.1671420.13175585X-RAY DIFFRACTION99
1.3603-1.41470.15881410.13215551X-RAY DIFFRACTION99
1.4147-1.47910.14661410.12925542X-RAY DIFFRACTION99
1.4791-1.55710.15021440.12145622X-RAY DIFFRACTION100
1.5571-1.65470.15111430.12735591X-RAY DIFFRACTION99
1.6547-1.78240.15881420.14065608X-RAY DIFFRACTION99
1.7824-1.96180.15431420.14825593X-RAY DIFFRACTION99
1.9618-2.24560.15721440.14895659X-RAY DIFFRACTION99
2.2456-2.82910.16871450.17345643X-RAY DIFFRACTION98
2.8291-35.57870.16231500.16635909X-RAY DIFFRACTION99

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