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- PDB-4mdy: Crystal structure of periplasmic solute binding protein from Myco... -

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Basic information

Entry
Database: PDB / ID: 4mdy
TitleCrystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155
ComponentsPeriplasmic binding protein
KeywordsTRANSPORT PROTEIN / MCSG / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / Protein Structure Initiative / ABC transporter system / solute binding protein
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Periplasmic binding protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsChang, C. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of periplasmic solute binding protein from Mycobacterium smegmatis str. MC2 155
Authors: Chang, C. / Wu, R. / Endres, M. / Joachimiak, A.
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5992
Polymers31,4931
Non-polymers1061
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.606, 90.449, 33.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Periplasmic binding protein / Periplasmic iron-transport lipoprotein


Mass: 31493.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_0438, MSMEI_0427 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: A0QPL3
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M Sodium Citrate, 0.1 M Phosphate-citrate, 20 % PEG 8000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 25588 / Num. obs: 24908 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 23.1
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.92 / Num. unique all: 1170 / % possible all: 97.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.78→31.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.729 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.128
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 1113 5 %RANDOM
Rwork0.1463 ---
all0.149 22242 --
obs0.149 22242 87.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.07 Å2 / Biso mean: 25.3141 Å2 / Biso min: 11.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2---1.75 Å2-0 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.78→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 7 199 2351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022249
X-RAY DIFFRACTIONr_bond_other_d0.0010.022157
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.9713082
X-RAY DIFFRACTIONr_angle_other_deg0.72134963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2225292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03324.73795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77215335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5771514
X-RAY DIFFRACTIONr_chiral_restr0.0560.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_rigid_bond_restr1.80734405
X-RAY DIFFRACTIONr_sphericity_free29.141569
X-RAY DIFFRACTIONr_sphericity_bonded8.52254486
LS refinement shellResolution: 1.779→1.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 59 -
Rwork0.162 946 -
all-1005 -
obs-1005 54.98 %

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