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- PDB-4me3: 1.8 Angstrom Crystal Structure of the N-terminal Domain of an Arc... -

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Basic information

Entry
Database: PDB / ID: 4me3
Title1.8 Angstrom Crystal Structure of the N-terminal Domain of an Archaeal MCM
ComponentsDNA replication licensing factor MCM related protein
KeywordsREPLICATION / AAA+ / Zinc binding domain / Helicase
Function / homology
Function and homology information


DNA replication initiation / DNA binding / ATP binding / metal ion binding
Similarity search - Function
mini-chromosome maintenance (MCM) complex, chain A, domain 1 / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / Rubrerythrin, domain 2 - #10 / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. ...mini-chromosome maintenance (MCM) complex, chain A, domain 1 / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / Rubrerythrin, domain 2 - #10 / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Rubrerythrin, domain 2 / Single Sheet / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA replication licensing factor MCM related protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å
AuthorsFu, Y. / Slaymaker, I.M. / Wang, G. / Chen, X.S.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The 1.8- angstrom Crystal Structure of the N-Terminal Domain of an Archaeal MCM as a Right-Handed Filament.
Authors: Fu, Y. / Slaymaker, I.M. / Wang, J. / Wang, G. / Chen, X.S.
History
DepositionAug 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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: DNA replication licensing factor MCM related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5192
Polymers31,4531
Non-polymers651
Water3,315184
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.460, 93.460, 56.231
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DNA replication licensing factor MCM related protein / minichromosome maintenance / MCM


Mass: 31453.480 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-262)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0799 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HK10
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.2 M magnesium chloride, 15% PEG400, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.9
SYNCHROTRONAPS 23-ID-D20.9
Detector
TypeIDDetector
ADSC QUANTUM 315r1CCD
MARMOSAIC 300 mm CCD2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.794→30 Å / Num. obs: 26333 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 22.24 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.299 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.794-1.8312.40.5413340.5641,2100
1.83-1.8612.40.42912880.6071,2100
1.86-1.912.40.36713070.6381,2100
1.9-1.9412.40.30113070.6651,2100
1.94-1.9812.50.23513030.7181,2100
1.98-2.0312.40.1812980.7771,2100
2.03-2.0812.50.17313210.8211,2100
2.08-2.1312.40.1413030.8931,2100
2.13-2.212.50.1213340.9691,2100
2.2-2.2712.50.11712861.1091,2100
2.27-2.3512.40.10413231.3191,2100
2.35-2.4412.50.09613121.4491,2100
2.44-2.5512.30.0913021.7681,2100
2.55-2.6912.40.0913161.9341,2100
2.69-2.8612.30.09113241.9641,2100
2.86-3.0812.30.08213082.291,2100
3.08-3.3912.10.07213342.5091,2100
3.39-3.8812.30.0613241.9331,2100
3.88-4.8812.20.04713351.5781,2100
4.88-3011.80.04113741.5121,299.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.794→26.98 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8622 / SU ML: 0.16 / σ(F): 0 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 1981 7.64 %
Rwork0.1817 --
obs0.1844 25918 98.5 %
all-27899 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.6 Å2 / Biso mean: 28.5617 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: LAST / Resolution: 1.794→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 1 184 2228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032085
X-RAY DIFFRACTIONf_angle_d0.7252809
X-RAY DIFFRACTIONf_chiral_restr0.048308
X-RAY DIFFRACTIONf_plane_restr0.003366
X-RAY DIFFRACTIONf_dihedral_angle_d12.599795
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.794-1.83930.23031330.19621624175794
1.8393-1.8890.23531360.18441640177695
1.889-1.94460.21741340.19441687182197
1.9446-2.00740.21771430.17691672181598
2.0074-2.07910.24051460.18451728187499
2.0791-2.16230.22311420.17951695183799
2.1623-2.26070.22921400.1841709184999
2.2607-2.37980.21311390.17261732187199
2.3798-2.52880.22271450.17891728187399
2.5288-2.72390.21791390.18681711185099
2.7239-2.99760.23811440.193617371881100
2.9976-3.43070.2341440.187517381882100
3.4307-4.31940.17181400.165917551895100
4.3194-26.98260.22491560.185617811937100

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