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- PDB-4gdn: Structure of FmtA-like protein -

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Basic information

Entry
Database: PDB / ID: 4gdn
TitleStructure of FmtA-like protein
ComponentsProtein flp
KeywordsHYDROLASE / peptidase / alpha/beta
Function / homology
Function and homology information


: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCougnoux, A. / Gibold, L. / Delmas, J. / Robin, F. / Dalmasso, G. / Bonnet, R.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Analysis of Structure-Function Relationships in the Colibactin-Maturating Enzyme ClbP.
Authors: Cougnoux, A. / Gibold, L. / Robin, F. / Dubois, D. / Pradel, N. / Darfeuille-Michaud, A. / Dalmasso, G. / Delmas, J. / Bonnet, R.
History
DepositionAug 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein flp
B: Protein flp
C: Protein flp
D: Protein flp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,1645
Polymers154,8104
Non-polymers3541
Water63135
1
A: Protein flp


Theoretical massNumber of molelcules
Total (without water)38,7021
Polymers38,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein flp


Theoretical massNumber of molelcules
Total (without water)38,7021
Polymers38,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein flp


Theoretical massNumber of molelcules
Total (without water)38,7021
Polymers38,7021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein flp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0572
Polymers38,7021
Non-polymers3541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.710, 179.710, 287.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein
Protein flp / FmtA-like protein


Mass: 38702.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: flp, SA2230 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7A3Q5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 4.33 Å3/Da / Density % sol: 71.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium acetate, 0.1M sodium acetate trihydrate, 30% W/v polyethylene glycol 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.2→85.76 Å / Num. obs: 42000 / % possible obs: 97.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.2
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.2 / Num. unique all: 42000 / % possible all: 98.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O3V

3o3v


Resolution: 3.2→85.73 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.842 / Cross valid method: THROUGHOUT / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29503 2217 5 %RANDOM
Rwork0.25733 ---
obs0.25921 42000 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.071 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.2→85.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10590 0 24 35 10649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210851
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.94214713
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.13651328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15326.008511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.725151898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.991516
X-RAY DIFFRACTIONr_chiral_restr0.1120.21643
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218156
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1461.56647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.898210783
X-RAY DIFFRACTIONr_scbond_it0.8634204
X-RAY DIFFRACTIONr_scangle_it1.5554.53930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 167 -
Rwork0.33 3088 -
obs--98.19 %

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