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- PDB-4mlz: Crystal structure of periplasmic binding protein from Jonesia den... -

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Basic information

Entry
Database: PDB / ID: 4mlz
TitleCrystal structure of periplasmic binding protein from Jonesia denitrificans
ComponentsPeriplasmic binding protein
Keywordssolute binding protein / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / ABC Transporter solute Binding Protein
Function / homology
Function and homology information


ABC transporter, F420-0 import, periplasmic substrate-binding protein, predicted / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Periplasmic binding protein
Similarity search - Component
Biological speciesJonesia denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsChang, C. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of periplasmic binding protein from Jonesia denitrificans
Authors: Chang, C. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic binding protein
B: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,50814
Polymers70,0302
Non-polymers47812
Water10,863603
1
A: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2146
Polymers35,0151
Non-polymers1995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2948
Polymers35,0151
Non-polymers2797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.678, 72.741, 71.306
Angle α, β, γ (deg.)90.000, 101.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic binding protein


Mass: 35014.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jonesia denitrificans (bacteria) / Strain: DSM 20603 / Gene: Jden_0967 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C7R301
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M CaCl2, 0.1M Tris, 25% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 2, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. all: 63028 / Num. obs: 62981 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 19.9
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2.09 / Num. unique all: 3151 / % possible all: 99.3

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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: 1.72→35.8 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.576 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3158 5.1 %RANDOM
Rwork0.1351 ---
all0.138 62314 --
obs0.138 62314 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.69 Å2 / Biso mean: 18.5384 Å2 / Biso min: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0 Å2-0.37 Å2
2---0.83 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.72→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 12 603 5071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024624
X-RAY DIFFRACTIONr_bond_other_d0.0010.024276
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9776358
X-RAY DIFFRACTIONr_angle_other_deg0.7723.0019900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0425612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23225.538186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.86615682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6161522
X-RAY DIFFRACTIONr_chiral_restr0.0740.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02914
X-RAY DIFFRACTIONr_rigid_bond_restr2.21638900
X-RAY DIFFRACTIONr_sphericity_free30.6655130
X-RAY DIFFRACTIONr_sphericity_bonded10.06459286
LS refinement shellResolution: 1.724→1.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 210 -
Rwork0.195 4164 -
all-4374 -
obs-4374 94.13 %

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