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- PDB-3fwx: The crystal structure of the peptide deformylase from Vibrio chol... -

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Basic information

Entry
Database: PDB / ID: 3fwx
TitleThe crystal structure of the peptide deformylase from Vibrio cholerae O1 biovar El Tor str. N16961
ComponentsPeptide deformylase
KeywordsHYDROLASE / peptide deformylase / structural genomics / CSGID / NIAID Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


co-translational protein modification / peptide deformylase / peptide deformylase activity / translation / metal ion binding
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Peptide deformylase / Peptide deformylase 1
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Zhou, M. / Stam, J. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of the peptide deformylase from Vibrio cholerae O1 biovar El Tor
Authors: Zhang, R. / Zhou, M. / Stam, J. / Anderson, W. / Joachimiak, A.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Peptide deformylase
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8504
Polymers38,7192
Non-polymers1312
Water5,206289
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4252
Polymers19,3601
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4252
Polymers19,3601
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.305, 61.456, 210.343
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
11A-314-

HOH

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Components

#1: Protein Peptide deformylase


Mass: 19359.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Strain: str. N16961 / Gene: def-1, GI:15640078, VC0395_A2473 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A5F4B3, UniProt: Q9KVU3*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10mM Sodium citrate, 33% PEG 6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→105.41 Å / Num. all: 26026 / Num. obs: 25897 / % possible obs: 99.54 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 14.72
Reflection shellResolution: 2→2.052 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2035 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→105.41 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.186 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.9 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.18
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26234 1368 5 %RANDOM
Rwork0.20204 ---
obs0.20506 25897 99.54 %-
all-26026 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 2 289 2911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222654
X-RAY DIFFRACTIONr_bond_other_d0.0010.021820
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9883592
X-RAY DIFFRACTIONr_angle_other_deg1.11634468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1495328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08525.152132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28615500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1161522
X-RAY DIFFRACTIONr_chiral_restr0.150.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
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_it1.1021.51648
X-RAY DIFFRACTIONr_mcbond_other0.3471.5658
X-RAY DIFFRACTIONr_mcangle_it1.90422684
X-RAY DIFFRACTIONr_scbond_it3.32831006
X-RAY DIFFRACTIONr_scangle_it5.4174.5908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 106 -
Rwork0.227 1929 -
obs-2035 100 %
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)
10.40070.2154-0.56850.5936-0.24631.64420.0455-0.0356-0.0080.0932-0.0267-0.0411-0.01710.1572-0.01880.04550.0108-0.03890.0618-0.00940.100526.9354.34171.051
20.65670.2135-0.2930.3427-0.6621.6646-0.02120.0951-0.0379-0.04690.0485-0.00830.1802-0.0117-0.02730.11270.0131-0.00890.0327-0.03710.12456.9053.67586.76
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 167
4X-RAY DIFFRACTION2B3 - 50
5X-RAY DIFFRACTION2B51 - 100
6X-RAY DIFFRACTION2B101 - 167

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