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- PDB-3m03: Crystal structure of human Orc6 fragment -

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Basic information

Entry
Database: PDB / ID: 3m03
TitleCrystal structure of human Orc6 fragment
ComponentsOrigin recognition complex subunit 6
KeywordsDNA BINDING PROTEIN / helix turn helix / Origin recognition complex / DNA replication
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / DNA replication initiation / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / fibrillar center ...CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / DNA replication initiation / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / fibrillar center / Orc1 removal from chromatin / DNA binding / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Origin recognition complex, subunit 6, metazoa/plant / : / ORC6 second cyclin-like domain / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Cyclin-like / Cyclin A; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Origin recognition complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.5 Å
AuthorsLiu, S.X. / Wu, L.J. / Sun, J. / Wang, H.F. / Liu, Y.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural analysis of human Orc6 protein reveals a homology with transcription factor TFIIB
Authors: Liu, S.X. / Balasov, M. / Wang, H.F. / Wu, L.J. / Chesnokov, I.N. / Liu, Y.F.
History
DepositionMar 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _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 6
B: Origin recognition complex subunit 6
C: Origin recognition complex subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7535
Polymers31,4623
Non-polymers2912
Water1,04558
1
A: Origin recognition complex subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6832
Polymers10,4871
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Origin recognition complex subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5832
Polymers10,4871
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Origin recognition complex subunit 6


Theoretical massNumber of molelcules
Total (without water)10,4871
Polymers10,4871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.571, 104.571, 30.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Origin recognition complex subunit 6 / ORC6


Mass: 10487.373 Da / Num. of mol.: 3 / Fragment: Middle Domain, reisdues 93-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC6 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y5N6
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, Li2SO4, PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 12005 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 38.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1226 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / SU B: 20.211 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.517 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26618 572 4.8 %RANDOM
Rwork0.22599 ---
obs0.2279 11398 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 17 58 2176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222130
X-RAY DIFFRACTIONr_angle_refined_deg1.3992.0112849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4615269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22625.8973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.08215450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.268159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021444
X-RAY DIFFRACTIONr_mcbond_it1.1071.51362
X-RAY DIFFRACTIONr_mcangle_it1.96822192
X-RAY DIFFRACTIONr_scbond_it3.3453768
X-RAY DIFFRACTIONr_scangle_it5.294.5657
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 37 -
Rwork0.313 854 -
obs-1226 100 %
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)
14.55440.32670.94332.8044-0.86214.8695-0.1380.10890.3740.0916-0.0657-0.2669-0.53970.78290.20370.1252-0.1111-0.02820.27160.03210.085332.074621.496428.1548
22.08160.3820.18855.84030.24781.8924-0.018-0.016-0.329-0.01210.01860.07620.04720.2989-0.00060.01540.03670.02210.13760.04360.185420.07290.221330.735
318.4373-3.79862.68595.28720.27192.183-0.21331.0534-0.13510.27760.26610.0302-0.2157-0.1461-0.05280.31180.0025-0.00620.80470.09430.431258.841910.432133.4452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 186
2X-RAY DIFFRACTION2B93 - 187
3X-RAY DIFFRACTION3C97 - 185

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