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- PDB-2zc2: Crystal structure of DnaD-like replication protein from Streptoco... -

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Basic information

Entry
Database: PDB / ID: 2zc2
TitleCrystal structure of DnaD-like replication protein from Streptococcus mutans UA159, gi 24377835, residues 127-199
ComponentsDnaD-like replication protein
KeywordsREPLICATION / replication protein / DnaD-like / gi 24377835 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DnaD domain-like / DnaD domain / DnaD-like domain superfamily / Replication initiation and membrane attachment / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DnaB_2 domain-containing protein
Similarity search - Component
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsDuke, N.E.C. / Clancy, S. / Duggan, E. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of DnaD-like replication protein from Streptococcus mutans UA159.
Authors: Duke, N.E.C. / Clancy, S. / Duggan, E. / Joachimiak, A.
History
DepositionNov 2, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DnaD-like replication protein
B: DnaD-like replication protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,85911
Polymers18,2702
Non-polymers5899
Water93752
1
A: DnaD-like replication protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3975
Polymers9,1351
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DnaD-like replication protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4626
Polymers9,1351
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.701, 81.701, 52.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DnaD-like replication protein


Mass: 9134.942 Da / Num. of mol.: 2 / Fragment: Residues 127-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans UA159 (bacteria) / Species: Streptococcus mutans / Strain: UA159 / Serotype c / Gene: SMU_1465c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8DT97
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% v/v 1,4-butanediol, 0.1M Imidazole, 0.2M Zinc acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionRedundancy: 8.8 % / Av σ(I) over netI: 11.7 / Number: 200964 / Rmerge(I) obs: 0.06 / Χ2: 1.03 / D res high: 2 Å / D res low: 50 Å / Num. obs: 22797 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.835099.310.0180.70210.1
5.436.8310010.0240.72510.4
4.745.4310010.0220.69210.5
4.314.7410010.0220.73210.5
44.3110010.0240.72810.4
3.76410010.0260.7459.7
3.583.7610010.0280.8239.3
3.423.5810010.0360.9449.6
3.293.4210010.0441.0339.7
3.173.2910010.0511.1839.8
3.083.1710010.0611.3019.9
2.993.0810010.0681.3059.8
2.912.9910010.0781.3359.8
2.842.9110010.0871.2899.8
2.772.8410010.1031.2669.8
2.712.7710010.1041.2099.6
2.662.7110010.1151.1349.6
2.612.6610010.1141.1759.5
2.562.6110010.131.1129.4
2.522.5610010.1341.099.2
2.482.5210010.1541.1129.2
2.442.4810010.1431.0518.9
2.412.4410010.161.0958.9
2.372.4110010.1581.1128.7
2.342.3710010.1691.0768.6
2.312.3410010.1721.0328.6
2.282.3110010.2311.0548.5
2.252.2899.710.2141.0528.4
2.232.2599.810.2251.0458.2
2.22.2399.810.2321.0098.3
2.182.29910.2650.9817.9
2.152.1899.110.251.0438
2.132.1598.510.31.0567.7
2.112.1398.710.3121.0157.7
2.092.1198.510.3290.9977.4
2.072.0996.910.3421.0017
2.052.0796.710.3791.036.6
2.032.0596.210.461.0116
2.022.0394.110.4591.0495.8
22.029310.5270.9975.3
ReflectionResolution: 2→50 Å / Num. obs: 22797 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.06 / Χ2: 1.031 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.02 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.527 / Num. unique all: 559 / Χ2: 0.997 / % possible all: 93

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.1 Å / D res low: 50 Å / FOM : 0.213 / FOM acentric: 0.257 / FOM centric: 0 / Reflection: 10802 / Reflection acentric: 8962 / Reflection centric: 1840
Phasing MAD setR cullis acentric: 1.53 / R cullis centric: 1 / Highest resolution: 2.1 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 8962 / Reflection centric: 1840
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.98-501.580.60.32237
7.46-12.981.670.50.313096
5.23-7.462.290.40.1344148
4.03-5.231.120.20.2656208
3.28-4.031.120.10.11081257
2.76-3.282.13001590313
2.39-2.762.7002218372
2.1-2.391.29002921409
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se48.157930.5040.3340.0250
2Se77.869120.5360.6240.0420
3Se41.174960.320.1620.0060
4Se44.652110.8340.520.0690
5Se57.943920.570.6350.020
6Se54.0970.3650.543-0.0070
7Se75.56010.3570.521-0.0090
8Se62.631440.2010.7050.0770
9Se75.578950.4880.9070.0390
10Se60.559790.2420.1330.0080
11Se81.698750.2970.2320.010
12Se72.271070.1190.160.0760
13Se52.954570.3610.2030.1230
14Se109.77730.0370.5050.0540
15Se47.083110.3180.4960.0260
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.98-500.2290.6140592237
7.46-12.980.3520.612022613096
5.23-7.460.3830.5480492344148
4.03-5.230.4170.5490864656208
3.28-4.030.3940.488013381081257
2.76-3.280.2760.33019031590313
2.39-2.760.1530.178025902218372
2.1-2.390.0650.074033302921409
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 10802
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.11-100700.652503
4.78-6.11630.848507
4.15-4.7862.50.892506
3.75-4.1561.90.893509
3.47-3.7561.30.911502
3.25-3.4762.80.87505
3.09-3.25610.871508
2.95-3.0965.80.879504
2.83-2.9570.30.873507
2.73-2.8367.90.866506
2.64-2.7373.90.887511
2.56-2.6472.70.855503
2.49-2.5669.60.897513
2.43-2.4975.70.857509
2.37-2.4376.20.898503
2.32-2.3778.80.88507
2.27-2.3279.50.874504
2.23-2.2779.30.869508
2.19-2.2380.10.856512
2.15-2.1980.90.864521
2.1-2.1585.90.816654

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.1→40.86 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.883 / SU B: 4.991 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Bijvoet differences were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 518 4.8 %RANDOM
Rwork0.243 ---
obs0.246 10802 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2--0.64 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 9 52 1313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221274
X-RAY DIFFRACTIONr_angle_refined_deg1.721.9561724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4185152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.70224.32474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97215236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9781514
X-RAY DIFFRACTIONr_chiral_restr0.1360.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02988
X-RAY DIFFRACTIONr_nbd_refined0.2220.2556
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2887
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.266
X-RAY DIFFRACTIONr_metal_ion_refined0.1780.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2270.22
X-RAY DIFFRACTIONr_mcbond_it1.4281.5783
X-RAY DIFFRACTIONr_mcangle_it2.22721220
X-RAY DIFFRACTIONr_scbond_it3.7023567
X-RAY DIFFRACTIONr_scangle_it5.724.5502
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 40 -
Rwork0.229 724 -
all-764 -
obs--98.45 %

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