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- PDB-4cij: Structure of Rolling Circle Replication Initiator Protein from Ge... -

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Basic information

Entry
Database: PDB / ID: 4cij
TitleStructure of Rolling Circle Replication Initiator Protein from Geobacillus stearothermophilus.
ComponentsGST REP
KeywordsISOMERASE / CELL CYCLE / ROLLING CIRCLE REPLICATION / ANTIBIOTIC RESISTANCE / TYPE I TOPOISOMERASE
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsCarr, S.B. / Phillips, S.E.V. / Thomas, C.D.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structures of Replication Initiation Proteins from Staphylococcal Antibiotic Resistance Plasmids Reveal Protein Asymmetry and Flexibility are Necessary for Replication.
Authors: Carr, S.B. / Phillips, S.E. / Thomas, C.D.
History
DepositionDec 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GST REP
B: GST REP
C: GST REP
D: GST REP


Theoretical massNumber of molelcules
Total (without water)125,5124
Polymers125,5124
Non-polymers00
Water3,945219
1
B: GST REP
D: GST REP


Theoretical massNumber of molelcules
Total (without water)62,7562
Polymers62,7562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-11.2 kcal/mol
Surface area25140 Å2
MethodPISA
2
A: GST REP
C: GST REP


Theoretical massNumber of molelcules
Total (without water)62,7562
Polymers62,7562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-11.9 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.111, 136.848, 149.157
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
GST REP


Mass: 31378.123 Da / Num. of mol.: 4 / Fragment: DNA RELAXASE DOMAIN, RESIDUES 2-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Strain: TK015 / Description: NARUMI ET AL. BIOTECH LETT 15, 815-820 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / Variant (production host): PLYSS / References: EC: 5.99.1.2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN CORRESPONDS TO TRANSLATION OF NUCLEOTIDES 794-1597 OF D29979

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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: 2.69 Å3/Da / Density % sol: 54.3 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M PROLINE, 0.1 M HEPES PH 7.5, 10 % (V/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 30, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.3→40.2 Å / Num. obs: 60795 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.9
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.3→40.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 13.812 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23457 3077 5.1 %RANDOM
Rwork0.19296 ---
obs0.19503 57652 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.222 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--1.35 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8720 0 0 219 8939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198910
X-RAY DIFFRACTIONr_bond_other_d0.0080.028638
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9512026
X-RAY DIFFRACTIONr_angle_other_deg1.271319806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17351064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54224.036446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.525151616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3511560
X-RAY DIFFRACTIONr_chiral_restr0.0870.21300
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210036
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022148
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.21742
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.27539
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.2148
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0410.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7646.3744268
X-RAY DIFFRACTIONr_mcbond_other4.7616.3724267
X-RAY DIFFRACTIONr_mcangle_it6.7879.5475328
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7016.9064642
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.47110.1076698
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 246 -
Rwork0.275 4160 -
obs--98.72 %
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)
10.4121-0.3280.37960.77430.08980.7678-0.00380.05620.00310.16290.0045-0.0193-0.00640.1034-0.00070.1775-0.0222-0.03030.03450.0130.05447.498536.089141.2757
20.68-0.3078-0.20130.72790.17820.2776-0.0275-0.02860.0292-0.09380.0873-0.0524-0.1509-0.0135-0.05980.2120.00230.01780.0188-0.00420.04220.490718.716878.7311
31.0484-0.60890.36050.5618-0.04770.82530.2218-0.0244-0.2378-0.0172-0.04960.20830.1894-0.2009-0.17220.1396-0.0636-0.06930.06440.04380.187823.814621.207425.7119
41.1384-0.11040.14730.62780.21610.1946-0.05880.076-0.24070.02050.0380.0083-0.0251-0.02970.02080.1288-0.0230.06010.0545-0.06270.116921.7049-12.298968.906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 267
2X-RAY DIFFRACTION2B0 - 267
3X-RAY DIFFRACTION3C3 - 267
4X-RAY DIFFRACTION4D-1 - 266

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