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- PDB-4r7y: Crystal structure of an active MCM hexamer -

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Basic information

Entry
Database: PDB / ID: 4r7y
TitleCrystal structure of an active MCM hexamer
ComponentsMinichromosome maintenance protein MCM, Cell division control protein 21
KeywordsHYDROLASE / AAA+ / OB-fold / MCM / helicase / ATPase / DNA replication
Function / homology
Function and homology information


MCM complex / intein-mediated protein splicing / DNA duplex unwinding / helicase activity / single-stranded DNA binding / endonuclease activity / DNA helicase / DNA replication / cell division / ATP hydrolysis activity ...MCM complex / intein-mediated protein splicing / DNA duplex unwinding / helicase activity / single-stranded DNA binding / endonuclease activity / DNA helicase / DNA replication / cell division / ATP hydrolysis activity / DNA binding / ATP binding / identical protein 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 / : / MCM protein C-terminal winged helix-turn-helix domain / Rubrerythrin, domain 2 - #10 / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region ...mini-chromosome maintenance (MCM) complex, chain A, domain 1 / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / : / MCM protein C-terminal winged helix-turn-helix domain / Rubrerythrin, domain 2 - #10 / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Intein N-terminal splicing region / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / Intein N-terminal splicing motif profile. / minichromosome maintenance proteins / MCM domain / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Rubrerythrin, domain 2 / Single Sheet / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA helicase / Minichromosome maintenance protein MCM
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
Pyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMiller, J.M. / Arachea, B.T. / Epling, L.B. / Enemark, E.J.
CitationJournal: Elife / Year: 2014
Title: Analysis of the crystal structure of an active MCM hexamer.
Authors: Miller, J.M. / Arachea, B.T. / Epling, L.B. / Enemark, E.J.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Nov 19, 2014Group: Database references
Revision 1.4Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.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.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_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: Minichromosome maintenance protein MCM, Cell division control protein 21
B: Minichromosome maintenance protein MCM, Cell division control protein 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,19114
Polymers138,9452
Non-polymers1,24712
Water0
1
A: Minichromosome maintenance protein MCM, Cell division control protein 21
B: Minichromosome maintenance protein MCM, Cell division control protein 21
hetero molecules

A: Minichromosome maintenance protein MCM, Cell division control protein 21
B: Minichromosome maintenance protein MCM, Cell division control protein 21
hetero molecules

A: Minichromosome maintenance protein MCM, Cell division control protein 21
B: Minichromosome maintenance protein MCM, Cell division control protein 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)420,57442
Polymers416,8346
Non-polymers3,74036
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area39150 Å2
ΔGint-338 kcal/mol
Surface area157040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.902, 118.902, 199.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Minichromosome maintenance protein MCM, Cell division control protein 21 /


Mass: 69472.336 Da / Num. of mol.: 2 / Fragment: Chimera fusion of SsoMCM-N and PfMCM-AAA
Source method: isolated from a genetically manipulated source
Details: Constructed as Sumo fusion (Mossessova and Lima, 2000)
Source: (gene. exp.) Sulfolobus solfataricus (archaea), (gene. exp.) Pyrococcus furiosus (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2, ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
Gene: MCM, SSO0774, PF0482 / Plasmid: pRSF-duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q9UXG1, UniProt: Q8U3I4, DNA helicase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl

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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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 10.8 mg/mL Sso-PfMCM; 5 mM ADP mixed 1:1 with 100 mM HEPES, pH 7.6; 350 mM MgCl2; 3 % (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Apr 5, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 43407 / Num. obs: 43329 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.107 / Net I/σ(I): 14.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.79 / Num. unique all: 4313 / Rsym value: 0.75 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SsoMCM N-terminal domain (2VL6), PfMCM ATPase domain (related entry 4R7Z)

2vl6

4r7z


Resolution: 2.7→49.83 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3602734.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1976 5.1 %RANDOM
Rwork0.263 ---
obs0.263 39044 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.0577 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 61.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å20 Å20 Å2
2---2.32 Å20 Å2
3---4.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9430 0 64 0 9494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.752.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 123 5.7 %
Rwork0.36 2042 -
obs-2042 50.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6adp.paramadp.top

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