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- PDB-1a12: REGULATOR OF CHROMOSOME CONDENSATION (RCC1) OF HUMAN -

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Basic information

Entry
Database: PDB / ID: 1a12
TitleREGULATOR OF CHROMOSOME CONDENSATION (RCC1) OF HUMAN
ComponentsREGULATOR OF CHROMOSOME CONDENSATION 1
KeywordsGUANINE NUCLEOTIDE EXCHANGE FACTOR / GEF / RAN / RAS-LIKE NUCLEAR GTP BINDING PROTEIN
Function / homology
Function and homology information


mitotic nuclear membrane reassembly / sulfate binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / regulation of mitotic nuclear division / nucleosome binding / spindle assembly / viral process / nucleosomal DNA binding ...mitotic nuclear membrane reassembly / sulfate binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / regulation of mitotic nuclear division / nucleosome binding / spindle assembly / viral process / nucleosomal DNA binding / mitotic spindle organization / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / chromosome segregation / small GTPase binding / G1/S transition of mitotic cell cycle / chromosome / histone binding / protein heterodimerization activity / cell division / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / Regulator of chromosome condensation (RCC1) signature 1. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 7 Propeller / Methylamine Dehydrogenase; Chain H / Mainly Beta
Similarity search - Domain/homology
Regulator of chromosome condensation
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE ISOMORPHOUS REPLACEMENT (SIR) COMBINED WITH 3-FOLD NCS AVERAGING / Resolution: 1.7 Å
AuthorsRenault, L. / Nassar, N. / Vetter, I. / Becker, J. / Roth, M. / Wittinghofer, A.
CitationJournal: Nature / Year: 1998
Title: The 1.7 A crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller.
Authors: Renault, L. / Nassar, N. / Vetter, I. / Becker, J. / Klebe, C. / Roth, M. / Wittinghofer, A.
History
DepositionDec 19, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REGULATOR OF CHROMOSOME CONDENSATION 1
B: REGULATOR OF CHROMOSOME CONDENSATION 1
C: REGULATOR OF CHROMOSOME CONDENSATION 1


Theoretical massNumber of molelcules
Total (without water)132,3293
Polymers132,3293
Non-polymers00
Water15,925884
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.957, 82.903, 83.105
Angle α, β, γ (deg.)112.88, 104.09, 103.42
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9853, -0.08662, 0.147246), (0.086682, -0.48923, -0.867836), (0.147209, 0.867843, -0.47453)0.4443, -0.1007, -1.5991
2given(0.98793, 0.139508, 0.067314), (0.014811, -0.517654, 0.855462), (0.154189, -0.84414, -0.513472)-0.7151, -1.0794, -1.4704

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Components

#1: Protein REGULATOR OF CHROMOSOME CONDENSATION 1 / RCC1


Mass: 44109.777 Da / Num. of mol.: 3 / Fragment: FULL LENGTH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTAC / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P18754
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 41 %
Description: NATIVE DATA SET OBTAINED BY MERGING 3 NATIVE DATA SETS, TWO COLLECTED ON ROTATING ANODE AND ONE COLLECTED AT DESY.
Crystal growpH: 6.9 / Details: pH 6.9
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096
DetectorDate: May 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9096 Å / Relative weight: 1
ReflectionResolution: 1.7→41.5 Å / Num. obs: 113006 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 23.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.257 / % possible all: 69.9
Reflection
*PLUS
Num. measured all: 596594
Reflection shell
*PLUS
% possible obs: 69.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: SINGLE ISOMORPHOUS REPLACEMENT (SIR) COMBINED WITH 3-FOLD NCS AVERAGING
Resolution: 1.7→41 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1000000 / Data cutoff low absF: 750.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 11010 10 %RANDOM
Rwork0.189 ---
obs0.189 110012 92 %-
Displacement parametersBiso mean: 17.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 0 884 3884
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.99
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.61.5
X-RAY DIFFRACTIONx_mcangle_it2.612
X-RAY DIFFRACTIONx_scbond_it2.642
X-RAY DIFFRACTIONx_scangle_it4.072.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.7→1.73 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 302 10 %
Rwork0.264 2725 -
obs--50.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.99
LS refinement shell
*PLUS
Rfactor obs: 0.264

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