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- PDB-2vl6: STRUCTURAL ANALYSIS OF THE SULFOLOBUS SOLFATARICUS MCM PROTEIN N-... -

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Basic information

Entry
Database: PDB / ID: 2vl6
TitleSTRUCTURAL ANALYSIS OF THE SULFOLOBUS SOLFATARICUS MCM PROTEIN N- TERMINAL DOMAIN
ComponentsMINICHROMOSOME MAINTENANCE PROTEIN MCM
KeywordsDNA BINDING PROTEIN / MCM / HELICASE / HYDROLASE / ZINC-FINGER / ATP-BINDING / DNA-BINDING / SSDNA BINDING / DNA REPLICATION / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


MCM complex / single-stranded DNA binding / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / ATP hydrolysis activity / ATP binding / identical protein 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 / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein ...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 / 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 / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Minichromosome maintenance protein MCM
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, W. / Pucci, B. / Rossi, M. / Pisani, F.M. / Ladenstein, R.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structural Analysis of the Sulfolobus Solfataricus Mcm Protein N-Terminal Domain.
Authors: Liu, W. / Pucci, B. / Rossi, M. / Pisani, F.M. / Ladenstein, R.
History
DepositionJan 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 4, 2013Group: Derived calculations / Other / Source and taxonomy
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MINICHROMOSOME MAINTENANCE PROTEIN MCM
B: MINICHROMOSOME MAINTENANCE PROTEIN MCM
C: MINICHROMOSOME MAINTENANCE PROTEIN MCM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6266
Polymers93,4293
Non-polymers1963
Water68538
1
A: MINICHROMOSOME MAINTENANCE PROTEIN MCM
B: MINICHROMOSOME MAINTENANCE PROTEIN MCM
C: MINICHROMOSOME MAINTENANCE PROTEIN MCM
hetero molecules

A: MINICHROMOSOME MAINTENANCE PROTEIN MCM
B: MINICHROMOSOME MAINTENANCE PROTEIN MCM
C: MINICHROMOSOME MAINTENANCE PROTEIN MCM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,25112
Polymers186,8596
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17300 Å2
ΔGint-59.8 kcal/mol
Surface area72670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.994, 52.236, 115.574
Angle α, β, γ (deg.)90.00, 124.15, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNVALVAL1AA7 - 967 - 96
21GLNGLNVALVAL1BB7 - 967 - 96
31GLNGLNVALVAL1CC7 - 967 - 96
12HISHISSERSER2AA97 - 26597 - 265
22HISHISSERSER2BB97 - 26597 - 265
32HISHISSERSER2CC97 - 26597 - 265

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.558123, -0.027933, 0.829288), (0.00676, 0.999553, 0.029119), (-0.829731, -0.010646, 0.558062)2.225, -0.47, 0.209
2given(0.463548, -0.012719, -0.885981), (0.028614, 0.99959, 0.000621), (0.88561, -0.025639, 0.463722)1.491, -0.525, -1.112

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Components

#1: Protein MINICHROMOSOME MAINTENANCE PROTEIN MCM / SSO MCM N-TER


Mass: 31143.121 Da / Num. of mol.: 3 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-29A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9UXG1
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.6 Å3/Da / Density % sol: 52.6 % / Description: NONE
Crystal growpH: 5.5
Details: 20% PEG 3350, 0.2 M MAGNESIUM CHLORIDE, 0.1 M SODIUM ACETATE, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 26, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→31.9 Å / Num. obs: 24102 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 18.38 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.07
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.35 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LTL

1ltl


Resolution: 2.8→31.88 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.894 / SU B: 38.201 / SU ML: 0.353 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMODELING OF RESIDUES 7-189 IS NEEDED AFTER MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1226 5.1 %RANDOM
Rwork0.233 ---
obs0.236 22821 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.18 Å2
2---0.21 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.8→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6348 0 3 38 6389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9878757
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0325774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92424.554303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.56151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0491548
X-RAY DIFFRACTIONr_chiral_restr0.1190.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024800
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2640.23024
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3320.24518
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4020.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4821.54006
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81626429
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54232734
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5994.52328
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A758tight positional0.060.05
12B758tight positional0.040.05
13C758tight positional0.040.05
21A676tight positional0.080.05
22B676tight positional0.080.05
23C676tight positional0.070.05
21A683medium positional0.30.5
22B683medium positional0.330.5
23C683medium positional0.30.5
11A758tight thermal0.090.5
12B758tight thermal0.060.5
13C758tight thermal0.070.5
21A676tight thermal0.10.5
22B676tight thermal0.110.5
23C676tight thermal0.110.5
21A683medium thermal0.752
22B683medium thermal0.712
23C683medium thermal0.652
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.485 92
Rwork0.396 1683
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)
111.9689-0.826-0.77098.81522.64035.9902-0.0567-1.2990.64251.2074-0.1909-0.01860.1545-0.31580.24770.1972-0.0536-0.070.1571-0.0976-0.01439.9552-3.305151.2624
26.58921.99734.64.99682.24365.3799-0.2453-0.20470.36740.10270.1127-0.4059-0.32890.0850.1327-0.03670.0408-0.0053-0.03930.0095-0.03577.7966-4.401139.911
31.9672.9058-0.671429.1105-8.71472.9618-0.2822-0.04880.7952-0.30680.3170.0538-0.4002-0.2232-0.03480.17890.0029-0.0027-0.0228-0.07050.095515.10447.763819.0393
412.4412.66180.52085.25352.37744.2931-0.24280.3441-0.0523-0.72850.08910.3429-0.0529-0.13220.1537-0.0434-0.0386-0.0303-0.1459-0.0534-0.14270.5903-12.554727.9823
517.48382.54372.47047.18674.966613.2798-0.0286-2.51530.63750.4968-0.98821.1843-0.3077-2.15171.01680.2035-0.02790.14471.2686-0.3310.2737-38.0063-3.608534.819
65.21320.38280.30981.2271-0.20699.8185-0.1019-1.40560.48290.0937-0.3691-0.0606-0.684-0.90460.4710.00950.05410.00970.4646-0.04480.0706-29.8373-4.602126.6554
75.293610.29710.021328.5863-1.56681.1187-0.21540.02110.3209-0.36840.2401-0.0778-0.8588-0.3394-0.02480.25590.1246-0.06280.0603-0.00030.1241-8.48337.783221.3546
83.4327-2.24843.0628.06542.35189.77140.1117-0.0472-0.2791-0.7513-0.2543-0.7023-0.4244-0.26320.1426-0.1390.00980.07020.028-0.00430.0144-24.0849-12.350413.8282
910.8952.2624-0.252611.047-4.296412.5580.368-1.51840.04881.062-1.5413-3.1433-1.07612.24641.17340.2646-0.4303-0.23760.8350.51.335450.3385-4.534517.0151
105.92560.2249-1.34464.8525-0.97465.09870.03380.08320.4747-0.3833-0.5544-1.5237-0.61931.36770.52060.1236-0.18320.03210.30410.23530.443939.5454-5.032113.423
111.8942-6.91761.501932.0554-11.20596.00940.074-0.11190.35790.09020.24520.6084-0.61080.0055-0.31930.1421-0.0590.00930.0845-0.07310.049723.86877.77-2.7522
128.08231.8635-4.64958.06560.08338.06530.15420.1103-0.005-0.1137-0.27530.2836-0.1697-0.03050.1211-0.1092-0.0877-0.0391-0.09920.0202-0.206625.0541-12.60614.2051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 68
2X-RAY DIFFRACTION2A69 - 128
3X-RAY DIFFRACTION3A129 - 194
4X-RAY DIFFRACTION4A195 - 265
5X-RAY DIFFRACTION5B7 - 68
6X-RAY DIFFRACTION6B69 - 128
7X-RAY DIFFRACTION7B129 - 194
8X-RAY DIFFRACTION8B195 - 265
9X-RAY DIFFRACTION9C7 - 68
10X-RAY DIFFRACTION10C69 - 128
11X-RAY DIFFRACTION11C129 - 194
12X-RAY DIFFRACTION12C195 - 265

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