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- PDB-2vn2: Crystal structure of the N-terminal domain of DnaD protein from G... -

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Basic information

Entry
Database: PDB / ID: 2vn2
TitleCrystal structure of the N-terminal domain of DnaD protein from Geobacillus kaustophilus HTA426
ComponentsCHROMOSOME REPLICATION INITIATION PROTEIN
KeywordsREPLICATION / DNAD / DNA REPLICATION / PRIMOSOME
Function / homology
Function and homology information


DnaD domain / DnaD-like domain superfamily / Replication initiation and membrane attachment / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chromosome replication initiation protein
Similarity search - Component
Biological speciesGEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsHuang, C.-Y. / Chang, Y.-W. / Chen, W.-T. / Sun, Y.-J. / Hsiao, C.-D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal Structure of the N-Terminal Domain of Geobacillus Kaustophilus Hta426 Dnad Protein.
Authors: Huang, C.-Y. / Chang, Y.-W. / Chen, W.-T.
History
DepositionJan 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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: CHROMOSOME REPLICATION INITIATION PROTEIN
B: CHROMOSOME REPLICATION INITIATION PROTEIN
C: CHROMOSOME REPLICATION INITIATION PROTEIN
D: CHROMOSOME REPLICATION INITIATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6408
Polymers58,5434
Non-polymers974
Water3,207178
1
A: CHROMOSOME REPLICATION INITIATION PROTEIN
C: CHROMOSOME REPLICATION INITIATION PROTEIN
hetero molecules

A: CHROMOSOME REPLICATION INITIATION PROTEIN
C: CHROMOSOME REPLICATION INITIATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6408
Polymers58,5434
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area11350 Å2
ΔGint-128.8 kcal/mol
Surface area19080 Å2
MethodPISA
2
B: CHROMOSOME REPLICATION INITIATION PROTEIN
D: CHROMOSOME REPLICATION INITIATION PROTEIN
hetero molecules

B: CHROMOSOME REPLICATION INITIATION PROTEIN
D: CHROMOSOME REPLICATION INITIATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6408
Polymers58,5434
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+3/2,y,-z+1/21
Buried area10680 Å2
ΔGint-80.9 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.514, 124.707, 157.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein
CHROMOSOME REPLICATION INITIATION PROTEIN / DNAD


Mass: 14635.804 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5KXY1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9794, 0.9795, 0.9643
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97951
30.96431
ReflectionResolution: 2.3→27.49 Å / Num. obs: 46920 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.59
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 9.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
Blu-IceCONTROL SOFTWAREdata reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.3→27.49 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 281278.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. RESIDUES GLU85 TO ASN94 AND GLY121 TO SER128 OF CHAIN A ARE DISORDERED. RESIDUES GLU85 TO ASN94 AND LEU120 TO SER128 OF CHAIN B ARE DISORDERED. RESIDUES MET1, GLU85 ...Details: BULK SOLVENT MODEL USED. RESIDUES GLU85 TO ASN94 AND GLY121 TO SER128 OF CHAIN A ARE DISORDERED. RESIDUES GLU85 TO ASN94 AND LEU120 TO SER128 OF CHAIN B ARE DISORDERED. RESIDUES MET1, GLU85 TO ASN94, AND GLY121 TO SER128 OF CHAIN C ARE DISORDERED. RESIDUES MET1, GLU85 TO ASN94, AND GLY121 TO SER128 OF CHAIN D ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 4573 9.7 %RANDOM
Rwork0.217 ---
obs0.217 46920 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8355 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.75 Å20 Å20 Å2
2--3.95 Å20 Å2
3---1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 4 178 3650
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.034
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.43
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.562
X-RAY DIFFRACTIONc_scangle_it3.792.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 654 8.6 %
Rwork0.229 6917 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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