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- PDB-4nnp: Crystal Structure of Apo Manganese ABC transporter MntC from Stap... -

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Basic information

Entry
Database: PDB / ID: 4nnp
TitleCrystal Structure of Apo Manganese ABC transporter MntC from Staphylococcus aureus bound to an antagonistic fab fragment
Components
  • Heavy chain of antagonistic fab fragment
  • Light chain of antagonistic fab fragment
  • Lipoprotein
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / ABC superfamily ATP binding cassette transporter / MntC / fab / Apo / MRSA / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold ...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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Lipoprotein / Lipoprotein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsRouge, L. / 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 1.0Dec 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein
B: Lipoprotein
H: Heavy chain of antagonistic fab fragment
X: Heavy chain of antagonistic fab fragment
L: Light chain of antagonistic fab fragment
Y: Light chain of antagonistic fab fragment


Theoretical massNumber of molelcules
Total (without water)163,6456
Polymers163,6456
Non-polymers00
Water4,468248
1
A: Lipoprotein
H: Heavy chain of antagonistic fab fragment
L: Light chain of antagonistic fab fragment


Theoretical massNumber of molelcules
Total (without water)81,8223
Polymers81,8223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-33 kcal/mol
Surface area31980 Å2
MethodPISA
2
B: Lipoprotein
X: Heavy chain of antagonistic fab fragment
Y: Light chain of antagonistic fab fragment


Theoretical massNumber of molelcules
Total (without water)81,8223
Polymers81,8223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-38 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.110, 92.510, 127.861
Angle α, β, γ (deg.)90.00, 92.48, 90.00
Int Tables number4
Space group name H-MP1211
DetailsOne molecule of MntC bound to Heavy chain and Light chain of a fab fragment.

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Components

#1: Protein Lipoprotein


Mass: 32890.176 Da / Num. of mol.: 2
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: Antibody Heavy chain of antagonistic fab fragment


Mass: 25374.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Light chain of antagonistic fab fragment


Mass: 23558.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris HCl pH 8.5, 20% PEG 10000 and 0.7% 1-Butanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 58231 / Num. obs: 58231 / % possible obs: 89.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 %

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→47.27 Å / SU ML: 0.46 / σ(F): 1.37 / Phase error: 32.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 2485 4.27 %
Rwork0.224 --
obs0.226 58231 88.9 %
all-58231 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11049 0 0 248 11297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111295
X-RAY DIFFRACTIONf_angle_d1.39115272
X-RAY DIFFRACTIONf_dihedral_angle_d14.5424136
X-RAY DIFFRACTIONf_chiral_restr0.0551682
X-RAY DIFFRACTIONf_plane_restr0.0071947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6832-2.73480.38361200.33312641X-RAY DIFFRACTION76
2.7348-2.79060.40191330.31583172X-RAY DIFFRACTION91
2.7906-2.85120.29281300.30353106X-RAY DIFFRACTION90
2.8512-2.91760.34751410.29533138X-RAY DIFFRACTION90
2.9176-2.99050.31851470.28213089X-RAY DIFFRACTION90
2.9905-3.07140.32681460.27193046X-RAY DIFFRACTION88
3.0714-3.16170.36691300.26472974X-RAY DIFFRACTION85
3.1617-3.26370.36841510.25053118X-RAY DIFFRACTION91
3.2637-3.38040.30021280.2413212X-RAY DIFFRACTION92
3.3804-3.51570.2821510.23063172X-RAY DIFFRACTION91
3.5157-3.67560.3121370.21623223X-RAY DIFFRACTION92
3.6756-3.86930.28941430.20243178X-RAY DIFFRACTION91
3.8693-4.11160.27581150.18912974X-RAY DIFFRACTION86
4.1116-4.42880.24311480.17973077X-RAY DIFFRACTION88
4.4288-4.87410.19151450.16813097X-RAY DIFFRACTION89
4.8741-5.57850.23911410.18953211X-RAY DIFFRACTION91
5.5785-7.02460.28621320.223179X-RAY DIFFRACTION90
7.0246-47.27390.26711470.23283139X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -7.7017 Å / Origin y: 23.2612 Å / Origin z: -10.3553 Å
111213212223313233
T0.0342 Å20.0273 Å2-0.0128 Å2--0.0268 Å2-0.0203 Å2--0.0246 Å2
L0.0377 °20.0309 °2-0.0455 °2-0.0866 °20.0023 °2--0.145 °2
S0.0207 Å °0.072 Å °-0.0141 Å °0.013 Å °-0.0043 Å °-0.0094 Å °-0.0149 Å °-0.0675 Å °0.0595 Å °
Refinement TLS groupSelection details: all

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