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- PDB-3fhw: Crystal structure of the protein priB from Bordetella parapertuss... -

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Basic information

Entry
Database: PDB / ID: 3fhw
TitleCrystal structure of the protein priB from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR162.
ComponentsPrimosomal replication protein n
KeywordsDNA BINDING PROTEIN / priB BpR162 X-RAY NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / DNA replication / DNA-binding / Primosome
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / single-stranded DNA binding
Similarity search - Function
Primosomal replication protein PriB / Another single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Primosomal replication protein N
Similarity search - Component
Biological speciesBordetella parapertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKuzin, A.P. / Neely, H. / Seetharaman, J. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Neely, H. / Seetharaman, J. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the protein priB from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR162.
Authors: Kuzin, A.P. / Neely, H. / Seetharaman, J. / Forouhar, F. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Primosomal replication protein n
B: Primosomal replication protein n
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5716
Polymers25,3962
Non-polymers1754
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-46 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.330, 64.320, 75.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-118-

HOH

Detailsdimer

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Components

#1: Protein Primosomal replication protein n


Mass: 12698.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis (bacteria) / Gene: priB, BPP2467 / References: UniProt: P67675
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 1.5M NaCl, 0.1M NaH2PO4, 0.1M KH2PO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 41038 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.3 / % possible all: 92.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→22.43 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.109 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Authors explanation on why Rfree/R are high at this resolution: The analyses of the Patterson function reveals a significant off-origin peak that is 56.98 % of the origin peak, indicating ...Details: Authors explanation on why Rfree/R are high at this resolution: The analyses of the Patterson function reveals a significant off-origin peak that is 56.98 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 2.5284e-05. The detected tranlational NCS is most likely also responsible for the elevated intensity ratio. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected.
RfactorNum. reflection% reflectionSelection details
Rfree0.28875 1006 5.2 %RANDOM
Rwork0.27544 ---
obs0.27613 18375 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.793 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 10 121 1625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221529
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2582.0142064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.55222.85756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70715285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.981516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021086
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.2629
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21029
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4230.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5711.5997
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12521589
X-RAY DIFFRACTIONr_scbond_it2.3323532
X-RAY DIFFRACTIONr_scangle_it3.7214.5472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 59 -
Rwork0.267 1042 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 31.1109 Å / Origin y: 14.653 Å / Origin z: 18.9432 Å
111213212223313233
T-0.0723 Å20.0017 Å20.0056 Å2--0.1525 Å2-0.0018 Å2---0.0343 Å2
L1.4752 °2-0.0024 °20.2561 °2-0.5986 °2-0.0285 °2--3.4684 °2
S0.0563 Å °0.0042 Å °0.1196 Å °0.0077 Å °-0.0172 Å °0.0001 Å °-0.132 Å °0.006 Å °-0.0391 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B118 - 182
2X-RAY DIFFRACTION1A118 - 175
3X-RAY DIFFRACTION1B116 - 117
4X-RAY DIFFRACTION1A116 - 117
5X-RAY DIFFRACTION1B1 - 102
6X-RAY DIFFRACTION1A1 - 102

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