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- PDB-1rzn: Crystal Structure of Penicillin-binding protein-related factor A ... -

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Basic information

Entry
Database: PDB / ID: 1rzn
TitleCrystal Structure of Penicillin-binding protein-related factor A from Bacillus Subtilis.
ComponentsRecombination protein U
KeywordsDNA BINDING PROTEIN / DNA repair / DNA recombination / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


crossover junction endodeoxyribonuclease / chromosome segregation / endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA 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
Holliday junction resolvase RecU
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.302 Å
AuthorsRamagopal, U.A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Penicillin-binding protein-related factor A from Bacillus Subtilis.
Authors: Ramagopal, U.A. / Almo, S.C.
History
DepositionDec 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Recombination protein U
B: Recombination protein U


Theoretical massNumber of molelcules
Total (without water)47,7282
Polymers47,7282
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-14 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.303, 74.303, 155.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLYSLYSAA33 - 5533 - 55
21THRTHRLYSLYSBB33 - 5533 - 55
32LEULEUPHEPHEAA112 - 145112 - 145
42LEULEUPHEPHEBB112 - 145112 - 145
53SERSERPHEPHEAA165 - 197165 - 197
63SERSERPHEPHEBB165 - 197165 - 197

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Components

#1: Protein Recombination protein U / Penicillin-binding protein-related factor A / PBP related factor A


Mass: 23863.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: RECU, PRFA, BSU22310 / Production host: Escherichia coli (E. coli) / References: UniProt: P39792
#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: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9B11.54
SYNCHROTRONNSLS X6A21.28322
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 15, 2003
ADSC QUANTUM 42CCDNov 10, 2003
RadiationMonochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
21.283221
ReflectionResolution: 2.302→30 Å / Num. all: 17965 / Num. obs: 17965 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 2.302→24.33 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.888 / SU B: 5.915 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.24507 969 5.1 %RANDOM
Rwork0.18603 ---
obs0.18897 17959 87.9 %-
all-17959 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.442 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.302→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 0 80 2607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222589
X-RAY DIFFRACTIONr_bond_other_d0.0020.022233
X-RAY DIFFRACTIONr_angle_refined_deg2.1861.9373491
X-RAY DIFFRACTIONr_angle_other_deg1.05335240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6685296
X-RAY DIFFRACTIONr_chiral_restr0.1350.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022840
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02548
X-RAY DIFFRACTIONr_nbd_refined0.2250.2502
X-RAY DIFFRACTIONr_nbd_other0.2510.22497
X-RAY DIFFRACTIONr_nbtor_other0.0920.21419
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.26
X-RAY DIFFRACTIONr_mcbond_it3.2131496
X-RAY DIFFRACTIONr_mcangle_it5.00552429
X-RAY DIFFRACTIONr_scbond_it6.01761093
X-RAY DIFFRACTIONr_scangle_it8.16781062
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
535medium positional0.20.5
882loose positional0.555
535medium thermal4.072
882loose thermal6.7610
LS refinement shellResolution: 2.302→2.361 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.203 56
Rwork0.153 1044

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