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- PDB-2chq: Replication Factor C ADPNP complex -

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Basic information

Entry
Database: PDB / ID: 2chq
TitleReplication Factor C ADPNP complex
ComponentsREPLICATION FACTOR C SMALL SUBUNIT
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / DNA REPLICATION / CLAMP LOADER / AAA+ ATPASE / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


DNA replication factor C complex / DNA clamp loader activity / DNA-templated DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Replication factor C small subunit, archaeal / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 ...Replication factor C small subunit, archaeal / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Replication factor C small subunit
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.5 Å
AuthorsSeybert, A. / Singleton, M.R. / Cook, N. / Hall, D.R. / Wigley, D.B.
CitationJournal: Embo J. / Year: 2006
Title: Communication between Subunits within an Archaeal Clamp-Loader Complex.
Authors: Seybert, A. / Singleton, M.R. / Cook, N. / Hall, D.R. / Wigley, D.B.
History
DepositionMar 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: REPLICATION FACTOR C SMALL SUBUNIT
B: REPLICATION FACTOR C SMALL SUBUNIT
C: REPLICATION FACTOR C SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6376
Polymers108,1193
Non-polymers1,5193
Water00
1
A: REPLICATION FACTOR C SMALL SUBUNIT
B: REPLICATION FACTOR C SMALL SUBUNIT
C: REPLICATION FACTOR C SMALL SUBUNIT
hetero molecules

A: REPLICATION FACTOR C SMALL SUBUNIT
B: REPLICATION FACTOR C SMALL SUBUNIT
C: REPLICATION FACTOR C SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,27512
Polymers216,2376
Non-polymers3,0376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)109.169, 109.169, 257.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24B
34C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEVALVAL1AA6 - 1616 - 161
21ILEILEVALVAL1BB6 - 1616 - 161
31ILEILEVALVAL1CC6 - 1616 - 161
12PROPROALAALA1AA162 - 224162 - 224
22PROPROALAALA1BB162 - 224162 - 224
32PROPROALAALA1CC162 - 224162 - 224
13ARGARGLYSLYS1AA227 - 318227 - 318
23ARGARGLYSLYS1BB227 - 318227 - 318
33ARGARGLYSLYS1CC227 - 318227 - 318
14ANPANPANPANP4AD700
24ANPANPANPANP4BE700
34ANPANPANPANP4CF700

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein REPLICATION FACTOR C SMALL SUBUNIT / REPLICATION FACTOR C / RFC SMALL SUBUNIT / CLAMP LOADER SMALL SUBUNIT / AFRFC SMALL SUBUNIT / AFRFCSM


Mass: 36039.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O28219
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.52 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 23090 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.06

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 3.5→95.35 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.9 / SU B: 97.45 / SU ML: 0.688 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.68
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.324 1175 5.1 %RANDOM
Rwork0.297 ---
obs0.299 21754 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 204.51 Å2
Baniso -1Baniso -2Baniso -3
1-4.84 Å22.42 Å20 Å2
2--4.84 Å20 Å2
3----7.25 Å2
Refinement stepCycle: LAST / Resolution: 3.5→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7419 0 93 0 7512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227632
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8471.99710308
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1555936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81323.739345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.646151413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2491569
X-RAY DIFFRACTIONr_chiral_restr0.1120.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025658
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2910.23958
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.25283
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2350
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.390.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0281.54772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.51327515
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.82533166
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11.694.52793
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1250tight positional0.050.05
12B1250tight positional0.040.05
13C1250tight positional0.040.05
21A474tight positional0.060.05
22B474tight positional0.060.05
23C474tight positional0.060.05
31A737tight positional0.060.05
32B737tight positional0.070.05
33C737tight positional0.060.05
41A31medium positional0.420.5
42B31medium positional0.340.5
43C31medium positional0.340.5
11A1250tight thermal0.070.5
12B1250tight thermal0.080.5
13C1250tight thermal0.080.5
21A474tight thermal0.150.5
22B474tight thermal0.130.5
23C474tight thermal0.120.5
31A737tight thermal0.160.5
32B737tight thermal0.140.5
33C737tight thermal0.130.5
41A31medium thermal0.792
42B31medium thermal0.772
43C31medium thermal0.512
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.369 77
Rwork0.395 1571
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)
112.57492.71863.95533.48070.32544.64850.4616-0.625-2.64830.4917-0.098-0.65030.94740.5237-0.3636-0.76090.2567-0.0517-0.55190.1487-0.143185.136525.78975.9064
25.8404-3.90544.89833.44950.421320.41580.7799-0.9399-0.449-0.7732-0.27711.58890.5325-1.1315-0.5028-1.07360.1838-0.0301-0.37560.0634-0.3333105.947945.390574.7914
31.1072-0.8445-1.89031.2611.91423.5890.00090.15680.0279-0.1898-0.09420.19010.2669-0.51520.0933-1.1404-0.0272-0.028-0.37810.0291-0.608394.371562.611757.291
41.87660.1448-0.92584.54596.827415.39720.3736-0.2664-0.93480.7565-0.54110.58022.9684-0.94220.1675-0.66080.0126-0.0384-0.67170.105-0.193954.076220.301461.6482
512.8148-0.4203-6.35051.0002-1.16725.0651-0.02320.6877-0.4689-0.24670.3250.02420.23-0.4938-0.3017-1.1324-0.0122-0.0768-0.33020.2105-0.45762.308738.366682.6359
63.1214-1.21-1.11750.4690.43320.40010.35880.215-0.0789-0.59960.00850.1766-0.3786-0.3024-0.3672-1.0325-0.02140.0368-0.52950.0288-0.578374.014957.354667.9763
76.8867-4.33221.642619.99911.48825.051-0.15730.6306-1.4268-0.80380.03421.95310.787-0.77880.1231-0.6557-0.2886-0.0687-0.99580.0164-0.175846.702714.206627.1788
815.4388-5.07635.94678.4472-10.16212.2271-0.33460.4062-1.5892-0.8945-0.3009-0.01530.96530.46980.6355-1.32190.04060.017-0.4965-0.0172-0.28236.743737.494241.5522
92.3448-0.70622.59240.2127-0.78072.866-0.19280.93060.3475-0.30420.2129-0.31050.18230.2096-0.02-1.13850.0674-0.0007-0.42640.0433-0.500357.477752.864251.542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 161
2X-RAY DIFFRACTION2A162 - 224
3X-RAY DIFFRACTION3A227 - 318
4X-RAY DIFFRACTION4B6 - 161
5X-RAY DIFFRACTION5B162 - 224
6X-RAY DIFFRACTION6B227 - 318
7X-RAY DIFFRACTION7C6 - 161
8X-RAY DIFFRACTION8C162 - 224
9X-RAY DIFFRACTION9C227 - 318

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