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- PDB-1m4z: Crystal structure of the N-terminal BAH domain of Orc1p -

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Basic information

Entry
Database: PDB / ID: 1m4z
TitleCrystal structure of the N-terminal BAH domain of Orc1p
ComponentsORIGIN RECOGNITION COMPLEX SUBUNIT 1
KeywordsGENE REGULATION / DNA replication / transcriptional silencing / chromatin / BAH domain
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / maintenance of rDNA / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nuclear pre-replicative complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex ...CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / maintenance of rDNA / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nuclear pre-replicative complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / silent mating-type cassette heterochromatin formation / DNA replication origin binding / DNA replication initiation / nucleosome binding / chromatin binding / ATP hydrolysis activity / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
Bromo adjacent homology (BAH) domain / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. ...Bromo adjacent homology (BAH) domain / : / Origin recognition complex subunit 1 C-terminal winged HTH domain / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / SH3 type barrels. / Roll / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
: / Origin recognition complex subunit 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, Z. / Hayashi, M.K. / Merkel, O. / Stillman, B. / Xu, R.-M.
CitationJournal: EMBO J. / Year: 2002
Title: Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing.
Authors: Zhang, Z. / Hayashi, M.K. / Merkel, O. / Stillman, B. / Xu, R.M.
History
DepositionJul 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: 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_ref_seq_dif / 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.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_ref_seq_dif.details / _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: ORIGIN RECOGNITION COMPLEX SUBUNIT 1
B: ORIGIN RECOGNITION COMPLEX SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4005
Polymers55,2352
Non-polymers1653
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ORIGIN RECOGNITION COMPLEX SUBUNIT 1
B: ORIGIN RECOGNITION COMPLEX SUBUNIT 1
hetero molecules

A: ORIGIN RECOGNITION COMPLEX SUBUNIT 1
B: ORIGIN RECOGNITION COMPLEX SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,80010
Polymers110,4704
Non-polymers3306
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area10660 Å2
ΔGint-56 kcal/mol
Surface area38650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.260, 61.050, 67.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-501-

MN

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Components

#1: Protein ORIGIN RECOGNITION COMPLEX SUBUNIT 1 / / ORIGIN RECOGNITION COMPLEX PROTEIN 120 KD SUBUNIT


Mass: 27617.506 Da / Num. of mol.: 2 / Fragment: BAH-containing Domain (RESIDUE 1-235)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Orc1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54784
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEGMME 2000, magnesium acetate, magnese chloride, MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 16 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MTris1reservoirpH7.5
228 %PEG2000 MME1reservoir
30.2 Mmagnesium acetate1reservoir
410 mM1reservoirMnCl2
510 %MPD1reservoir
630 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jan 1, 2000 / Details: morrors
RadiationMonochromator: silicon 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 27960 / Num. obs: 26610 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.5
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1141 / % possible all: 84
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Rmerge(I) obs: 0.111

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Processing

Software
NameClassification
PHASESphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2099 7.6 %random
Rwork0.2 ---
all0.225 26533 --
obs0.225 26533 --
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 3 266 3586
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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