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- PDB-1plq: CRYSTAL STRUCTURE OF THE EUKARYOTIC DNA POLYMERASE PROCESSIVITY F... -

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Basic information

Entry
Database: PDB / ID: 1plq
TitleCRYSTAL STRUCTURE OF THE EUKARYOTIC DNA POLYMERASE PROCESSIVITY FACTOR PCNA
ComponentsPROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)
KeywordsDNA-BINDING / NUCLEAR PROTEIN / DNA REPLICATION / PROCESSIVITY FACTOR
Function / homology
Function and homology information


positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 ...positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / establishment of mitotic sister chromatid cohesion / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / DNA damage tolerance / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / Dual incision in TC-NER / translesion synthesis / subtelomeric heterochromatin formation / mismatch repair / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / nucleotide-excision repair / mitotic cell cycle / chromosome, telomeric region / DNA binding / identical protein binding / nucleus
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / 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 ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / 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
: / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsKrishna, T.S.R. / Kong, X.-P. / Gary, S. / Burgers, P.M. / Kuriyan, J.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA.
Authors: Krishna, T.S. / Kong, X.P. / Gary, S. / Burgers, P.M. / Kuriyan, J.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of Proliferating Cell Nuclear Antigen (PCNA) from Saccharomyces Cerevisiae
Authors: Krishna, T.S.R. / Kong, X.-P. / Gary, S. / Burgers, P. / Kuriyan, J.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Sliding Clamps of DNA Polymerases
Authors: Kuriyan, J. / Donnell, M.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: Three-Dimensional Structure of the Beta Subunit of E. Coli DNA Polymerase III Holoenzyme: A Sliding DNA Clamp
Authors: Kong, X.-P. / Onrust, R. / Donnell, M. / Kuriyan, J.
History
DepositionJan 2, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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.process_site / _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

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Assembly

Deposited unit
A: PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3453
Polymers28,9441
Non-polymers4012
Water2,108117
1
A: PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)
hetero molecules

A: PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)
hetero molecules

A: PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0369
Polymers86,8323
Non-polymers1,2046
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Unit cell
Length a, b, c (Å)121.200, 121.200, 121.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA)


Mass: 28944.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P15873
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE IS THAT OF THE MERCURY COMPLEX OF PCNA.
Nonpolymer detailsTHE STRUCTURE IS OF THE MERCURY COMPLEX OF THE PROTEIN INVOLVING TWO MERCURY ATOMS PER MONOMER. THE ...THE STRUCTURE IS OF THE MERCURY COMPLEX OF THE PROTEIN INVOLVING TWO MERCURY ATOMS PER MONOMER. THE FIRST MERCURY ATOM CROSSLINKS THE SIDE CHAINS OF CYS 30 AND CYS 62 BY FORMING COVALENT BONDS WITH SULFUR ATOMS OF THESE CYS RESIDUES. THE SECOND MERCURY IS BOUND TO CYS 22.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.13 Å3/Da / Density % sol: 76 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown / Details: Krishna, T.S.R., (1994) J.Mol.Biol., 241, 265.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl11
21 mMEDTA11
31 mMDTT11
40.1 M11NaCl
520 mg/mlprotain12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 26608 / % possible obs: 93.7 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Redundancy: 11.3 % / Num. measured all: 300303 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / % possible obs: 92.7 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→5 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.187 --
obs0.187 22454 92.5 %
Displacement parametersBiso mean: 34.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 2 117 2149
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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