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- PDB-5gxv: Crystal structure of PigG -

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Basic information

Entry
Database: PDB / ID: 5gxv
TitleCrystal structure of PigG
ComponentsMaltose-binding periplasmic protein,PigG
KeywordsPROTEIN TRANSPORT / PigG / Prodigiosin
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
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
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Serratia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsZhang, F. / Ran, T. / Xu, D. / Wang, W.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31400055 China
National Natural Science Foundation of China31170686 China
National Natural Science Foundation of China31100028 China
the Natural Science Foundation of Jiangsu ProvinceBK20140690 China
CitationJournal: Int. J. Biol. Macromol. / Year: 2017
Title: Crystal structure of MBP-PigG fusion protein and the essential function of PigG in the prodigiosin biosynthetic pathway in Serratia marcescens FS14.
Authors: Zhang, F. / Wei, Q. / Tong, H. / Xu, D. / Wang, W. / Ran, T.
History
DepositionSep 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,PigG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4152
Polymers51,3911
Non-polymers241
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.131, 55.131, 262.127
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

21A-666-

HOH

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Components

#1: Protein Maltose-binding periplasmic protein,PigG / MBP / MMBP / Maltodextrin-binding protein


Mass: 51390.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of MBP (RESIDURS 3-368) AND PigG (RESIDUES 369-468)
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Serratia (bacteria)
Strain: K12 / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE REFERENCE FOR RESIDUES 369-468 DOES NOT CURRENTLY EXIST IN UNP

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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: 45.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: MgCl2,Tris-HCl, pH 8.5, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: AREA DETECTOR / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28301 / % possible obs: 100 % / Redundancy: 19.3 % / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 20 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2247refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.1→47.745 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1378 4.89 %
Rwork0.1892 --
obs0.1913 28187 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 1 141 3663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083602
X-RAY DIFFRACTIONf_angle_d0.8224891
X-RAY DIFFRACTIONf_dihedral_angle_d15.0932150
X-RAY DIFFRACTIONf_chiral_restr0.049538
X-RAY DIFFRACTIONf_plane_restr0.005638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.26731230.2212646X-RAY DIFFRACTION100
2.1751-2.26210.30121370.21942588X-RAY DIFFRACTION100
2.2621-2.36510.271570.21372611X-RAY DIFFRACTION100
2.3651-2.48980.24221690.21742601X-RAY DIFFRACTION100
2.4898-2.64580.28881040.22322685X-RAY DIFFRACTION100
2.6458-2.850.28551080.21712664X-RAY DIFFRACTION100
2.85-3.13680.27091240.21742672X-RAY DIFFRACTION100
3.1368-3.59050.27851340.19412702X-RAY DIFFRACTION100
3.5905-4.52320.20281430.15562758X-RAY DIFFRACTION100
4.5232-47.75720.17761790.16822882X-RAY DIFFRACTION100

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