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- PDB-5zh8: Crystal Structure of FmtA from Staphylococcus aureus at 2.58 A -

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Basic information

Entry
Database: PDB / ID: 5zh8
TitleCrystal Structure of FmtA from Staphylococcus aureus at 2.58 A
ComponentsProtein FmtA
KeywordsHYDROLASE / Methicillin resistance / Penicillin binding protein / Carboxypeptidase Esterase
Function / homology
Function and homology information


teichoic acid D-alanine hydrolase / autolysis / positive regulation of single-species biofilm formation / cell wall organization / hydrolase activity / response to antibiotic / plasma membrane
Similarity search - Function
: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Teichoic acid D-alanine hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDalal, V. / Kumar, P. / Golemi-Kotra, D. / Kumar, P.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Repurposing an Ancient Protein Core Structure: Structural Studies on FmtA, a Novel Esterase of Staphylococcus aureus.
Authors: Dalal, V. / Kumar, P. / Rakhaminov, G. / Qamar, A. / Fan, X. / Hunter, H. / Tomar, S. / Golemi-Kotra, D. / Kumar, P.
History
DepositionMar 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FmtA
B: Protein FmtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4654
Polymers92,2812
Non-polymers1842
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-5 kcal/mol
Surface area29640 Å2
Unit cell
Length a, b, c (Å)105.391, 128.234, 107.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-557-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 46 - 396 / Label seq-ID: 46 - 396

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Protein FmtA


Mass: 46140.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: fmtA, fmt / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O50608
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.97 Å3/Da / Density % sol: 37.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M NaCl, 0.1 M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 22784 / % possible obs: 95.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 55.2 Å2 / CC1/2: 0.98 / Net I/σ(I): 13.28
Reflection shellResolution: 2.58→2.62 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.58 / % possible all: 28

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Processing

Software
NameVersionClassification
REFMAC5.8.0216refinement
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GDN

4gdn


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 34.194 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25436 1118 5 %RANDOM
Rwork0.20765 ---
obs0.20993 21118 97.56 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.79 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5779 0 12 136 5927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.025959
X-RAY DIFFRACTIONr_bond_other_d0.0010.025562
X-RAY DIFFRACTIONr_angle_refined_deg1.0321.9778028
X-RAY DIFFRACTIONr_angle_other_deg0.714313013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79825.092273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.535151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8681512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021170
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_it0.353.6862838
X-RAY DIFFRACTIONr_mcbond_other0.353.6862837
X-RAY DIFFRACTIONr_mcangle_it0.6465.5283544
X-RAY DIFFRACTIONr_mcangle_other0.6465.5293545
X-RAY DIFFRACTIONr_scbond_it0.2083.7083120
X-RAY DIFFRACTIONr_scbond_other0.2073.7083120
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4015.5464485
X-RAY DIFFRACTIONr_long_range_B_refined2.1342.1026762
X-RAY DIFFRACTIONr_long_range_B_other2.0642.046749
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11990 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 56 -
Rwork0.33 1239 -
obs--77.5 %
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)
13.9194-0.01861.32021.17340.04352.9179-0.1256-0.43270.13390.0243-0.03630.0975-0.0927-0.38080.16190.009-0.00860.0020.2799-0.08110.03115.96335.5254.632
22.1215-0.0350.3514.12240.89242.8167-0.2668-0.21610.7671-0.1663-0.19330.3734-0.8816-0.44230.46010.29750.1493-0.20340.4567-0.14220.377230.13859.18822.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 397
2X-RAY DIFFRACTION2B46 - 397

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