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- PDB-4pqk: C-Terminal domain of DNA binding protein -

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Basic information

Entry
Database: PDB / ID: 4pqk
TitleC-Terminal domain of DNA binding protein
ComponentsMaltose ABC transporter periplasmic protein, Truncated replication protein RepA
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Replication initiator protein A, C-terminal domain / Replication initiator protein A C-terminal domain / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / Truncated replication protein RepA / Maltose/maltodextrin-binding periplasmic protein / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.401 Å
AuthorsSchumacher, M.A. / Chinnam, N. / Tonthat, N.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein.
Authors: Schumacher, M.A. / Tonthat, N.K. / Kwong, S.M. / Chinnam, N.B. / Liu, M.A. / Skurray, R.A. / Firth, N.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 22, 2017Group: Refinement description / Category: 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.auth_asym_id / _atom_site.auth_atom_id ..._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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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 ABC transporter periplasmic protein, Truncated replication protein RepA
B: Maltose ABC transporter periplasmic protein, Truncated replication protein RepA
C: Maltose ABC transporter periplasmic protein, Truncated replication protein RepA
D: Maltose ABC transporter periplasmic protein, Truncated replication protein RepA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,8688
Polymers219,8504
Non-polymers2,0184
Water00
1
A: Maltose ABC transporter periplasmic protein, Truncated replication protein RepA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4672
Polymers54,9631
Non-polymers5041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose ABC transporter periplasmic protein, Truncated replication protein RepA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4672
Polymers54,9631
Non-polymers5041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Maltose ABC transporter periplasmic protein, Truncated replication protein RepA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4672
Polymers54,9631
Non-polymers5041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Maltose ABC transporter periplasmic protein, Truncated replication protein RepA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4672
Polymers54,9631
Non-polymers5041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.220, 93.668, 100.806
Angle α, β, γ (deg.)107.67, 108.30, 84.93
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Maltose ABC transporter periplasmic protein, Truncated replication protein RepA


Mass: 54962.527 Da / Num. of mol.: 4 / Fragment: unp residues 71-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Staphylococcus aureus (bacteria)
Strain: K-12 substr. MC4100 / Gene: malE, BN896_3748 / Production host: Escherichia coli (E. coli)
References: UniProt: U6NJU2, UniProt: B1B3N6, UniProt: P0AEX9*PLUS
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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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: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.1 M MES pH 6.5 and 0.2 Calcium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 28157 / Num. obs: 28157 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 73.91 Å2 / Rmerge(I) obs: 0.116 / Χ2: 0.521 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.4-3.462.10.24112460.677187
3.46-3.522.10.22813510.598188.4
3.52-3.592.10.21713370.556190.2
3.59-3.662.10.213390.605191.6
3.66-3.742.10.20214330.637194.6
3.74-3.832.20.18613850.605195.7
3.83-3.922.20.18914550.596196.4
3.92-4.032.30.17714420.596197.2
4.03-4.152.30.16914370.592196.8
4.15-4.282.30.1614890.667197.6
4.28-4.442.30.16214130.57197.9
4.44-4.612.40.14514400.557197.4
4.61-4.822.40.13514170.547195.9
4.82-5.082.50.12614590.542196.4
5.08-5.42.50.11414240.474196.2
5.4-5.812.50.10714290.507196.4
5.81-6.42.50.09514270.46195.5
6.4-7.322.60.08214080.383195.2
7.32-9.212.70.06314180.307195.4
9.21-502.80.05714080.252195.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.401→46.625 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7431 / SU ML: 0.5 / σ(F): 1.99 / Phase error: 33.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 1963 10.01 %
Rwork0.237 --
obs0.2409 19619 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.74 Å2 / Biso mean: 69.4185 Å2 / Biso min: 25.17 Å2
Refinement stepCycle: LAST / Resolution: 3.401→46.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14740 0 136 0 14876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915214
X-RAY DIFFRACTIONf_angle_d1.21520664
X-RAY DIFFRACTIONf_chiral_restr0.0552318
X-RAY DIFFRACTIONf_plane_restr0.0072649
X-RAY DIFFRACTIONf_dihedral_angle_d18.4685478
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 (%)
3.4008-3.48580.364320.258328731915
3.4858-3.580.3575500.239645150124
3.58-3.68530.3396700.241962369334
3.6853-3.80420.3042870.2279388042
3.8042-3.94010.25121090.2438970107952
3.9401-4.09780.27911290.23041169129862
4.0978-4.28420.25741470.23571320146769
4.2842-4.50990.27961620.22911462162478
4.5099-4.79220.26941830.21491637182087
4.7922-5.16170.29331930.22641742193594
5.1617-5.68040.2712000.23521794199495
5.6804-6.50040.271990.25711800199996
6.5004-8.18260.27352010.25351802200396
8.1826-46.6290.26322010.23781806200796

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