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- PDB-1y1o: X-ray crystal Structure of Penicillin-binding protein-related fac... -

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Basic information

Entry
Database: PDB / ID: 1y1o
TitleX-ray crystal Structure of Penicillin-binding protein-related factor A from Bacillus stearothermophilus
ComponentsPenicillin-binding protein-related factor A
KeywordsRECOMBINATION / structural genomics / Protein Structure Initiative / PSI / Midwest Center for Structural Genomics / MCSG / Penicillin-binding protein
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / chromosome segregation / endonuclease activity / DNA recombination / nucleic acid binding / DNA repair / magnesium ion binding / cytoplasm
Similarity search - Function
Holliday junction resolvase RecU / Recombination protein U / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Holliday junction resolvase RecU
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsOsipiuk, J. / Li, H. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal Structure of Penicillin-binding protein-related factor A from Bacillus stearothermophilus
Authors: Osipiuk, J. / Li, H. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionNov 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE THERE IS NO SUITABLE SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein-related factor A
B: Penicillin-binding protein-related factor A
C: Penicillin-binding protein-related factor A
D: Penicillin-binding protein-related factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,92717
Polymers93,7534
Non-polymers1,17413
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-224 kcal/mol
Surface area30740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.261, 81.018, 106.279
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
Penicillin-binding protein-related factor A / prfA / recU


Mass: 23438.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP1992 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5KXY4*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.9 Å3/Da / Density % sol: 33.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.3 M ammonium sulfate, 1% PEG 3350, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794255 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2004
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794255 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 36081 / Num. obs: 35057 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 17
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 1.42 / % possible all: 62

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→34.1 Å / Cor.coef. Fo:Fc: 0.947 / SU B: 8.842 / SU ML: 0.116 / σ(F): 0 / σ(I): 0 / ESU R: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 2038 -random
Rwork0.1973 ---
all0.1988 35030 --
obs0.1988 35030 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.593 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.66 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5512 0 57 144 5713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225700
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9427726
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9623.151292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32215956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4581544
X-RAY DIFFRACTIONr_chiral_restr0.1050.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.22380
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23799
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3590.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.131.53462
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69925416
X-RAY DIFFRACTIONr_scbond_it2.57932582
X-RAY DIFFRACTIONr_scangle_it4.0184.52310
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 115 -
Rwork0.234 1951 -
obs-1836 74.47 %

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