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- PDB-4m7o: The crystal structure of a possible an iron-binding (periplasmic ... -

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Basic information

Entry
Database: PDB / ID: 4m7o
TitleThe crystal structure of a possible an iron-binding (periplasmic solute-binding) protein from Staphylococcus epidermidis ATCC 12228.
ComponentsIron-binding protein
KeywordsIron binding protein / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyABC 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 / Iron-binding protein / Iron-binding protein
Function and homology information
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.02 Å
AuthorsTan, K. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible an iron-binding (periplasmic solute-binding) protein from Staphylococcus epidermidis ATCC 12228.
Authors: Tan, K. / Li, H. / Clancy, S. / Joachimiak, A.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-binding protein


Theoretical massNumber of molelcules
Total (without water)31,7361
Polymers31,7361
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.052, 48.173, 44.916
Angle α, β, γ (deg.)90.00, 102.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Iron-binding protein / periplasmic solute-binding protein


Mass: 31736.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: ATCC 12228 / Gene: SE_0383 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8CQ54, UniProt: A0A0H2VHB1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 6.5
Details: 0.1M MgCl2, 0.1M MES:NaOH, 30% (v/v) PEG400, pH 6.5, MICRODIALYSIS, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915, 0.97938
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2013 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979381
ReflectionResolution: 2.02→35 Å / Num. all: 20707 / Num. obs: 20707 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 3.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.5
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.9 / Num. unique all: 867 / % possible all: 81.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.02→34.72 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1060 5.13 %random
Rwork0.1804 ---
all0.1827 20669 --
obs0.1827 20669 96.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→34.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 0 80 2092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072040
X-RAY DIFFRACTIONf_angle_d0.9912745
X-RAY DIFFRACTIONf_dihedral_angle_d13.215784
X-RAY DIFFRACTIONf_chiral_restr0.067312
X-RAY DIFFRACTIONf_plane_restr0.005355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0198-2.11170.33021240.27422119X-RAY DIFFRACTION85
2.1117-2.22310.27891290.24012368X-RAY DIFFRACTION95
2.2231-2.36230.29441380.2222470X-RAY DIFFRACTION98
2.3623-2.54470.27281260.21152501X-RAY DIFFRACTION99
2.5447-2.80060.23421380.2012507X-RAY DIFFRACTION100
2.8006-3.20560.26031390.19952531X-RAY DIFFRACTION100
3.2056-4.03780.19811280.15992544X-RAY DIFFRACTION100
4.0378-34.72540.18271380.14622569X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7893-0.5546-0.83493.0153-1.08892.036-0.125-0.16660.39730.03290.1551-0.3554-0.11420.04080.06040.26220.0006-0.00860.1927-0.0090.280240.407522.622630.6126
28.08471.00991.67884.33480.52854.1701-0.19280.9601-0.6951-0.37130.2877-1.14820.08220.47680.01640.38290.0060.12310.4246-0.02150.561747.388612.571623.8661
36.36470.12860.10332.71360.42212.9723-0.1727-0.377-0.80280.3646-0.006-0.31540.4575-0.07610.19570.4026-0.00530.0060.21380.08350.287936.759611.179935.7567
44.11810.81121.93542.65520.11511.7455-0.2737-1.00150.58260.6857-0.18350.5241-0.2696-0.24590.44270.46040.05470.02110.6018-0.25420.252523.892126.877442.0652
56.7131-4.6705-3.44237.51863.61875.1396-0.2378-0.38520.1890.2334-0.21611.0255-0.076-0.63920.39960.2566-00.01140.3577-0.14180.57019.154112.595325.0509
64.2983-0.11131.25635.69651.84843.46860.1335-1.0820.18440.4499-0.24170.8097-0.0936-0.22730.08890.2731-0.020.06650.5324-0.06220.511511.894411.354533.1774
72.3267-0.20811.65763.32310.9323.57320.1964-0.2319-0.9256-0.2159-0.05770.47010.1901-0.14940.09030.2793-0.0165-0.04120.3153-0.08560.56756.79983.40222.4259
85.61431.44550.47433.24490.0593.81860.09490.46330.2185-0.4843-0.14870.6247-0.2448-0.01660.02740.35240.0354-0.11250.3207-0.05620.48139.698315.217815.3318
91.56080.46880.4221.6576-0.40973.406-0.23610.3853-0.2925-0.2753-0.38441.0175-0.4903-0.99740.82070.37190.0357-0.14810.5112-0.15830.81840.317113.9516.728
106.97453.3346.04731.59372.8925.2341-0.20810.46090.5271-0.07710.06840.37280.07630.34370.16630.3152-0.0375-0.03170.37130.00550.31821.376619.858325.2671
113.6922.4364.44485.49331.216.3326-0.11710.40351.5963-0.7096-0.54621.0630.13170.11670.70310.33170.0357-0.0160.4455-0.14270.576913.522725.089528.9415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 170 )
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 193 )
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 217 )
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 229 )
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 251 )
9X-RAY DIFFRACTION9chain 'A' and (resid 252 through 265 )
10X-RAY DIFFRACTION10chain 'A' and (resid 266 through 280 )
11X-RAY DIFFRACTION11chain 'A' and (resid 281 through 294 )

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