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- PDB-4jbz: Structure of Mcm10 coiled-coil region -

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Basic information

Entry
Database: PDB / ID: 4jbz
TitleStructure of Mcm10 coiled-coil region
ComponentsMALTOSE-BINDING PERIPLASMIC PROTEIN FUSED WITH XENOPUS LAEVIS MCM10 COILED-COIL REGION
KeywordsREPLICATION / COILED-COIL / THREE-HELIX BUNDLE / MINICHROMOSOME MAINTENANCE / DNA REPLICATION
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / DNA replication initiation / ATP-binding cassette (ABC) transporter complex ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / DNA replication initiation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / single-stranded DNA binding / outer membrane-bounded periplasmic space / double-stranded DNA binding / periplasmic space / DNA damage response / membrane / metal ion binding / nucleus
Similarity search - Function
Replication factor Mcm10, C-terminal / Mcm10 replication factor / Mcm10 replication factor / Zinc finger, Mcm10/DnaG-type / Minichromosome maintenance protein 10 / Primase zinc finger / Immunoglobulin FC, subunit C / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...Replication factor Mcm10, C-terminal / Mcm10 replication factor / Mcm10 replication factor / Zinc finger, Mcm10/DnaG-type / Minichromosome maintenance protein 10 / Primase zinc finger / Immunoglobulin FC, subunit C / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Nucleic acid-binding, OB-fold / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Protein MCM10 homolog
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDu, W. / Adhikary, S. / Eichman, B.F.
CitationJournal: Plos One / Year: 2013
Title: Mcm10 self-association is mediated by an N-terminal coiled-coil domain.
Authors: Du, W. / Josephrajan, A. / Adhikary, S. / Bowles, T. / Bielinsky, A.K. / Eichman, B.F.
History
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Other
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALTOSE-BINDING PERIPLASMIC PROTEIN FUSED WITH XENOPUS LAEVIS MCM10 COILED-COIL REGION
B: MALTOSE-BINDING PERIPLASMIC PROTEIN FUSED WITH XENOPUS LAEVIS MCM10 COILED-COIL REGION
C: MALTOSE-BINDING PERIPLASMIC PROTEIN FUSED WITH XENOPUS LAEVIS MCM10 COILED-COIL REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,4176
Polymers132,3903
Non-polymers1,0273
Water8,035446
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-38 kcal/mol
Surface area45640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.377, 116.618, 73.395
Angle α, β, γ (deg.)90.00, 103.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

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Components

#1: Protein MALTOSE-BINDING PERIPLASMIC PROTEIN FUSED WITH XENOPUS LAEVIS MCM10 COILED-COIL REGION


Mass: 44130.125 Da / Num. of mol.: 3
Fragment: MALTOSE-BINDING PERIPLASMIC PROTEIN: unp residues 27-392, XENOPUS LAEVIS MCM10 COILED-COIL REGION (RESIDUES 95-124)
Mutation: D82A, K83A, E172A, N173A, K239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Xenopus laevis (African clawed frog)
Strain: MS 21-1 / Gene: HMPREF9530_03068, Mcm10 / Plasmid: PMALXE / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P0AEX9, UniProt: Q5EAW4
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFUSION PROTEIN OF A MUTANT FORM OF MALTOSE-BINDING PERIPLASMIC PROTEIN AND REPLICATION FACTOR MCM10 ...FUSION PROTEIN OF A MUTANT FORM OF MALTOSE-BINDING PERIPLASMIC PROTEIN AND REPLICATION FACTOR MCM10 COILED COIL REGION WITH LINKER REGION NAAAMG. PDB RESIDUES 373-402 CORRESPOND TO XENOPUS LAEVIS MCM10 RESIDUES 95-124.

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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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.1M sodium acetate, 0.1M NaCl, 0.1M CaCl2, 15% PEG 2K,5% (w/v) N-dodecyl-beta-D-maltoside, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 289.15K

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Data collection

DiffractionMean temperature: 193.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2012
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 59496 / Num. obs: 59496 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.069
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.401 / % possible all: 94.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H4Z

3h4z


Resolution: 2.4→29.154 Å / SU ML: 0.23 / σ(F): 0.98 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2990 5.02 %random
Rwork0.1637 ---
obs0.1658 59488 98 %-
all-116760 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8865 0 69 446 9380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089144
X-RAY DIFFRACTIONf_angle_d1.10512490
X-RAY DIFFRACTIONf_dihedral_angle_d12.3983176
X-RAY DIFFRACTIONf_chiral_restr0.0671424
X-RAY DIFFRACTIONf_plane_restr0.0061619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.393-2.42020.23931760.20833271X-RAY DIFFRACTION87
2.4202-2.44860.28582150.20083530X-RAY DIFFRACTION93
2.4486-2.47850.27711900.19693492X-RAY DIFFRACTION95
2.4785-2.50980.24591440.19593641X-RAY DIFFRACTION94
2.5098-2.54290.25132050.1913569X-RAY DIFFRACTION95
2.5429-2.57770.23371710.18773622X-RAY DIFFRACTION96
2.5777-2.61450.2421740.18773614X-RAY DIFFRACTION95
2.6145-2.65350.24141690.17513626X-RAY DIFFRACTION96
2.6535-2.69490.27321850.18643669X-RAY DIFFRACTION97
2.6949-2.73910.19471990.18793633X-RAY DIFFRACTION97
2.7391-2.78630.25181980.19373735X-RAY DIFFRACTION98
2.7863-2.83690.25781790.18693784X-RAY DIFFRACTION99
2.8369-2.89140.25151810.18413703X-RAY DIFFRACTION99
2.8914-2.95040.22991930.18923786X-RAY DIFFRACTION99
2.9504-3.01440.23852200.18353707X-RAY DIFFRACTION100
3.0144-3.08450.23192130.17883798X-RAY DIFFRACTION100
3.0845-3.16150.20891750.19043803X-RAY DIFFRACTION100
3.1615-3.24690.25682220.18313755X-RAY DIFFRACTION100
3.2469-3.34230.22861900.18123801X-RAY DIFFRACTION100
3.3423-3.450.18132100.16743745X-RAY DIFFRACTION100
3.45-3.57310.20032250.16313696X-RAY DIFFRACTION100
3.5731-3.71590.21652130.16273789X-RAY DIFFRACTION100
3.7159-3.88470.18552060.15033767X-RAY DIFFRACTION100
3.8847-4.0890.19822120.14523769X-RAY DIFFRACTION100
4.089-4.34440.14161820.13293781X-RAY DIFFRACTION100
4.3444-4.67860.16751840.12833756X-RAY DIFFRACTION100
4.6786-5.14710.18311750.12623811X-RAY DIFFRACTION100
5.1471-5.88650.19352220.15753744X-RAY DIFFRACTION100
5.8865-7.39630.16952300.16453757X-RAY DIFFRACTION100
7.3963-29.15660.18052040.1523744X-RAY DIFFRACTION99
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)
11.273-0.086-0.01331.4397-0.47121.36980.0680.18-0.0738-0.11410.0393-0.07930.11960.132-0.08380.2046-0.00020.00580.233-0.05960.14015.593635.6204-19.3607
22.76260.42810.09261.59860.131.16620.0354-0.1580.24050.072-0.00380.3789-0.1221-0.2966-0.02470.28840.08420.02680.34460.02630.3699-36.490460.668-22.1466
32.85530.18-0.13532.32180.34051.33850.1492-0.2566-0.24210.2898-0.03220.35930.3004-0.2528-0.12780.4318-0.2005-0.07150.43210.04070.4372-37.613812.0146-17.4964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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