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- PDB-1ud9: Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Ho... -

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Basic information

Entry
Database: PDB / ID: 1ud9
TitleCrystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus tokodaii
ComponentsDNA polymerase sliding clamp A
KeywordsDNA BINDING PROTEIN / DNA-binding / DNA replication
Function / homology
Function and homology information


DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / DNA binding
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp 1
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.68 Å
AuthorsTanabe, E. / Yasutake, Y. / Tanaka, Y. / Yao, M. / Tsumoto, K. / Kumagai, I. / Tanaka, I.
CitationJournal: To be published
Title: Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) Homolog From Sulfolobus tokodaii
Authors: Tanabe, E. / Yasutake, Y. / Tanaka, Y. / Yao, M. / Tsumoto, K. / Kumagai, I. / Tanaka, I.
History
DepositionApr 28, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: DNA polymerase sliding clamp A
B: DNA polymerase sliding clamp A
C: DNA polymerase sliding clamp A
D: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,52127
Polymers109,0174
Non-polymers1,50423
Water8,269459
1
A: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7779
Polymers27,2541
Non-polymers5238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
2
B: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5165
Polymers27,2541
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
3
C: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5816
Polymers27,2541
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
4
D: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6477
Polymers27,2541
Non-polymers3926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
A: DNA polymerase sliding clamp A
hetero molecules

B: DNA polymerase sliding clamp A
C: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,87520
Polymers81,7633
Non-polymers1,11217
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_656x+1,y,z+11
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-688 kcal/mol
Surface area46130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.400, 75.440, 88.140
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA polymerase sliding clamp A / Proliferation cell nuclear antigen / PCNA


Mass: 27254.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q975N2
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CLEAR ELECTRON DENSITY SHOWS THE N-TERMINAL RESIDUE IS NOT MET BUT ALA. ACTUALLY THE ALANINE ...THE CLEAR ELECTRON DENSITY SHOWS THE N-TERMINAL RESIDUE IS NOT MET BUT ALA. ACTUALLY THE ALANINE WAS INSERTED BETWEEN THE FIRST MET AND SECOND HIS, BECAUSE THE PCNA-CODING INSERT DNA WAS DIGESTED WITH THE RESTRICTION ENZYME NCOI. IT SEEMS THAT THE FIRST MET WAS PROCESSED.

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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: 2.38 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3.75%(w/v) PEG8000, 0.1M MES, 0.2M Zn(OAc)2, 0.1M Glycine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2002 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 114482 / % possible obs: 97.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.2
Reflection shellResolution: 1.68→1.74 Å / Rmerge(I) obs: 0.398 / Num. unique all: 9574 / % possible all: 82.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNSrefinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.68→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 11301 9.7 %RANDOM
Rwork0.202 ---
all-113938 --
obs-113938 97.8 %-
Solvent computationSolvent model: THROUGHOUT / Bsol: 62.63 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 27.07 Å2
Baniso -1Baniso -2Baniso -3
1--2.607 Å20 Å20.686 Å2
2---4.01 Å20 Å2
3---6.618 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.68→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7514 0 23 459 7996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg2.09
X-RAY DIFFRACTIONc_dihedral_angle_d26.45
X-RAY DIFFRACTIONc_improper_angle_d1.48
X-RAY DIFFRACTIONc_mcbond_it1.56
X-RAY DIFFRACTIONc_mcangle_it2.355
X-RAY DIFFRACTIONc_scbond_it2.751
X-RAY DIFFRACTIONc_scangle_it4.082
LS refinement shellResolution: 1.68→1.74 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3316 922 7.96 %
Rwork0.3002 8534 -
obs-9456 81.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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