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- PDB-4toz: MppA Periplasmic Murein Tripeptide Binding Protein, Unliganded Op... -

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Open data


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Basic information

Entry
Database: PDB / ID: 4toz
TitleMppA Periplasmic Murein Tripeptide Binding Protein, Unliganded Open Form
ComponentsPeriplasmic murein peptide-binding protein
KeywordsPEPTIDE BINDING PROTEIN / periplasmic ligand binding protein / Murein Tripeptide Binding Protein
Function / homology
Function and homology information


peptidoglycan-associated peptide transport / tripeptide transport / oligopeptide binding / tripeptide import across plasma membrane / dipeptide transport / heme transmembrane transport / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein transport ...peptidoglycan-associated peptide transport / tripeptide transport / oligopeptide binding / tripeptide import across plasma membrane / dipeptide transport / heme transmembrane transport / peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / protein transport / outer membrane-bounded periplasmic space / periplasmic space / membrane
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Periplasmic murein peptide-binding protein MppA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsJeffery, C.J. / Bhatt, F.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association United States
CitationJournal: To Be Published
Title: Open Conformation of the E. coli Periplasmic Murein Tripeptide Binding Protein, MppA, at High Resolution
Authors: Bhatt, F. / Patel, V. / Jeffery, C.J.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic murein peptide-binding protein
B: Periplasmic murein peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6013
Polymers117,4792
Non-polymers1221
Water29,6711647
1
A: Periplasmic murein peptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8612
Polymers58,7391
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Periplasmic murein peptide-binding protein


Theoretical massNumber of molelcules
Total (without water)58,7391
Polymers58,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.970, 76.810, 89.570
Angle α, β, γ (deg.)90.000, 91.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic murein peptide-binding protein


Mass: 58739.270 Da / Num. of mol.: 2 / Fragment: UNP residues 23-537
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: mppA, ynaH, b1329, JW1322 / Production host: Escherichia coli (E. coli) / References: UniProt: P77348
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1647 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: drop contained 2 microliters of 10 mg/mL protein solution and 2 microliters of the reservoir solution containing 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. obs: 162196 / % possible obs: 99.6 % / Redundancy: 1.008 % / Net I/σ(I): 38.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CNSrefinement
PDB_EXTRACT3.14data extraction
AMoREphasing
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RKM

1rkm


Resolution: 1.5→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2055 7938 4.9 %
Rwork0.18 153654 -
obs-161592 99.6 %
Solvent computationBsol: 56.8983 Å2
Displacement parametersBiso max: 94.21 Å2 / Biso mean: 16.1 Å2 / Biso min: 3.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.943 Å20 Å2-0.259 Å2
2---1.945 Å20 Å2
3---1.002 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 8 1647 9803
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.251
X-RAY DIFFRACTIONc_mcbond_it1.0431.5
X-RAY DIFFRACTIONc_scbond_it1.8942
X-RAY DIFFRACTIONc_mcangle_it1.5922
X-RAY DIFFRACTIONc_scangle_it2.6732.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep2.paramprotein2.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5tris.paramtris.topology

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