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- PDB-3f9v: Crystal Structure Of A Near Full-Length Archaeal MCM: Functional ... -

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Basic information

Entry
Database: PDB / ID: 3f9v
TitleCrystal Structure Of A Near Full-Length Archaeal MCM: Functional Insights For An AAA+ Hexameric Helicase
ComponentsMinichromosome maintenance protein MCM
KeywordsHYDROLASE / Replicative Helicase / DNA Replication / MCM Complex / AAA+ Protein / ATP-binding / DNA-binding / Helicase / Nucleotide-binding
Function / homology
Function and homology information


MCM complex / helicase activity / single-stranded DNA binding / DNA helicase / DNA replication / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
: / MCM protein C-terminal winged helix-turn-helix domain / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain ...: / MCM protein C-terminal winged helix-turn-helix domain / MCM N-terminal domain / MCM N-terminal domain / 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 / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Minichromosome maintenance protein MCM
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.35 Å
AuthorsChen, X.J. / Brewster, A.S. / Wang, G.G. / Yu, X. / Greenleaf, W. / Tjajadi, M. / Klein, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal structure of a near-full-length archaeal MCM: Functional insights for an AAA+ hexameric helicase.
Authors: Brewster, A.S. / Wang, G. / Yu, X. / Greenleaf, W.B. / Carazo, J.M. / Tjajadia, M. / Klein, M.G. / Chen, X.S.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minichromosome maintenance protein MCM


Theoretical massNumber of molelcules
Total (without water)67,3191
Polymers67,3191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)202.526, 202.526, 128.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
DetailsA hexamer model can be created that aligns well with the N-terminal Methanobacterium thermoautotrophicum MCM hexamer (PDB ID 1LTL) using the following non-crystallographic matrices. Apply matrix 1 for monomer 1, and then apply the summation of matrix 1 and matrix N to create monomer N, where N is 2-6. 1) LSQ_RT_NTTONTAIMP R 12 (3f14.8) 0.43327817 0.61568034 0.65818518 -0.90081984 0.31867027 0.29491171 -0.02817271 -0.72068506 0.69268990 239.07376099 11.87045383 -79.62718964 2) LSQ_RT_ATOB2IMP R 12 (3f14.8) 0.50902790 -0.86062968 -0.01439116 0.86053950 0.50920200 -0.01360237 0.01903461 -0.00546018 0.99980390 -0.94980073 110.48052979 1.74927461 3) LSQ_RT_ATOCIMP R 12 (3f14.8) -0.49999857 0.86602622 -0.00000035 -0.86602622 -0.49999857 0.00000028 0.00000007 0.00000044 1.00000000 192.32089233 -0.00009566 0.00002129 4) LSQ_RT_ATODIMP R 12 (3f14.8) 0.49081263 0.87114632 -0.01439028 -0.87125200 0.49064746 -0.01360218 -0.00478894 0.01921368 0.99980396 97.11698151 -56.06281281 1.74919856 5) LSQ_RT_ATOEIMP R 12 (3f14.8) -0.49999991 -0.86602545 -0.00000097 0.86602545 -0.49999991 0.00000114 -0.00000147 -0.00000028 1.00000000 96.16052246 166.55490112 0.00005019 6) LSQ_RT_ATOFIMP R 12 (3f14.8) -0.99984115 -0.01051573 -0.01439001 0.01071160 -0.99985009 -0.01360323 -0.01424481 -0.01375521 0.99980390 192.31431580 112.13711548 1.74920392

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Components

#1: Protein Minichromosome maintenance protein MCM


Mass: 67318.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: MCM, SSO0774 / Plasmid: pGEX-Kg / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UXG1, Hydrolases

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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: 4.88 Å3/Da / Density % sol: 74.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50mM NaCl, 65mM CalCl2, 20% MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794 Å
DetectorType: ADSC / Detector: CCD / Date: Oct 29, 2007
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 4.35→30 Å / Num. obs: 7760

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 4.35→30 Å / Cor.coef. Fo:Fc: 0.832 / Cor.coef. Fo:Fc free: 0.803 / Occupancy max: 1 / Occupancy min: 1 / SU B: 349.255 / SU ML: 2.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.467
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: Proline residues identified in remark 500 as having deviant covalent bond angles were modeled as alanines in the structure. As such the standard values used as a reference against these ...Details: Proline residues identified in remark 500 as having deviant covalent bond angles were modeled as alanines in the structure. As such the standard values used as a reference against these residues are not relevant to a poly-alanine structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.481 343 4.6 %RANDOM
Rwork0.412 ---
obs0.415 7390 82.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 190.98 Å2 / Biso mean: 185.302 Å2 / Biso min: 181.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å20 Å20 Å2
2--3.86 Å20 Å2
3----7.73 Å2
Refinement stepCycle: LAST / Resolution: 4.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 0 2944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222943
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.8494100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1595594
X-RAY DIFFRACTIONr_chiral_restr0.0670.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022376
X-RAY DIFFRACTIONr_nbd_refined0.2880.21314
X-RAY DIFFRACTIONr_nbtor_refined0.2920.22077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.222
X-RAY DIFFRACTIONr_mcbond_it0.1391.52943
X-RAY DIFFRACTIONr_mcangle_it0.25224100
LS refinement shellResolution: 4.35→4.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.559 17 -
Rwork0.55 460 -
all-477 -
obs--75.83 %
Refinement TLS params.Method: refined / Origin x: -10.973 Å / Origin y: 168.9816 Å / Origin z: 52.6142 Å
111213212223313233
T-0.9178 Å20.0393 Å2-0.114 Å2--0.7669 Å2-0.3005 Å2---0.6781 Å2
L3.7553 °21.7535 °23.0788 °2-2.2413 °21.0675 °2--5.2606 °2
S0.0647 Å °-0.2036 Å °-0.1283 Å °0.3326 Å °0.1617 Å °-0.6413 Å °-0.3058 Å °0.73 Å °-0.2264 Å °

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