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- PDB-3ot4: Structure and Catalytic Mechanism of Bordetella bronchiseptica nicF -

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Basic information

Entry
Database: PDB / ID: 3ot4
TitleStructure and Catalytic Mechanism of Bordetella bronchiseptica nicF
ComponentsPutative isochorismatase
KeywordsHYDROLASE / Bordetella bronchiseptica / nicF / maleamate hydrolase
Function / homology
Function and homology information


Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isochorismatase / Putative isochorismatase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRowlett, R.S. / Snider, M.J.
CitationJournal: To be Published
Title: Structure and catalytic mechanism of Bordetella bronchisepta nicF
Authors: Rowlett, R.S. / Snider, M.J.
History
DepositionSep 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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_conn / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative isochorismatase
B: Putative isochorismatase
C: Putative isochorismatase
D: Putative isochorismatase
E: Putative isochorismatase
F: Putative isochorismatase
G: Putative isochorismatase
H: Putative isochorismatase


Theoretical massNumber of molelcules
Total (without water)202,1728
Polymers202,1728
Non-polymers00
Water7,837435
1
A: Putative isochorismatase
B: Putative isochorismatase
F: Putative isochorismatase
H: Putative isochorismatase


Theoretical massNumber of molelcules
Total (without water)101,0864
Polymers101,0864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint-60 kcal/mol
Surface area23940 Å2
MethodPISA
2
C: Putative isochorismatase
D: Putative isochorismatase
E: Putative isochorismatase
G: Putative isochorismatase


Theoretical massNumber of molelcules
Total (without water)101,0864
Polymers101,0864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-59 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.560, 157.560, 198.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Putative isochorismatase


Mass: 25271.492 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB0275, BB1782, nicF / Production host: Escherichia coli (E. coli)
References: UniProt: Q7TTE5, UniProt: A0A0H3LKK8*PLUS, EC: 3.5.1.107
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M cacodylic acid, 0.2 M ammonium acetate, 30% PEG-8000, 10 mg/mL protein in 10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Sep 6, 2010 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→12.01 Å / Num. obs: 68504 / % possible obs: 91.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.2 % / Rsym value: 0.087 / Net I/σ(I): 9.78
Reflection shellResolution: 2.4→2.52 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.271 / % possible all: 67.5

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Processing

Software
NameVersionClassification
CrysalisProdata collection
PHASERphasing
REFMAC5.5.0109refinement
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NBA

1nba


Resolution: 2.4→12.01 Å / Cor.coef. Fo:Fc: 0.848 / Cor.coef. Fo:Fc free: 0.771 / SU B: 23.942 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.459 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31097 1400 2 %RANDOM
Rwork0.24058 ---
obs0.24201 68504 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→12.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11740 0 0 435 12175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211988
X-RAY DIFFRACTIONr_bond_other_d0.0010.027900
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.95516308
X-RAY DIFFRACTIONr_angle_other_deg1.104319197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.1335.11593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13923480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.139151780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0311588
X-RAY DIFFRACTIONr_chiral_restr0.0860.21855
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022505
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_it0.4981.57847
X-RAY DIFFRACTIONr_mcbond_other0.0991.53229
X-RAY DIFFRACTIONr_mcangle_it0.859212450
X-RAY DIFFRACTIONr_scbond_it1.4534141
X-RAY DIFFRACTIONr_scangle_it2.2794.53858
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 74 -
Rwork0.272 3803 -
obs--76.3 %
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)
11.18570.49070.43741.22220.53591.0008-0.01520.03830.0415-0.2799-0.09610.0653-0.1451-0.04370.11130.13540.0408-0.02640.047-0.00990.022233.14543.7357.963
20.7386-0.0847-0.18580.55510.0540.7992-0.0439-0.04790.01290.13830.00320.0916-0.0116-0.10890.04070.0852-0.01410.03760.05-0.03290.048129.83747.11241.915
31.1773-0.1399-0.09510.34410.05640.6445-0.0233-0.157-0.09220.0054-0.0246-0.0185-0.01550.02450.04790.02870.00160.00230.090.04960.060654.282-2.82470.521
40.8415-0.15430.06680.71090.49380.55750.011-0.0620.0053-0.00910.0170.08630.0074-0.0852-0.0280.0277-0.0045-0.00210.05290.02790.098125.22211.54660.467
50.97160.042-0.07840.54090.20040.75780.02890.0174-0.0863-0.0349-0.0102-0.07030.00640.1025-0.01870.02690.00550.00630.05430.01510.056754.6564.99647.645
60.99740.5504-0.10650.5099-0.24520.6061-0.0395-0.0081-0.0210.06220.03520.01990.0187-0.10.00430.0597-0.00610.00830.05960.0080.044146.03261.68431.995
71.35920.74410.12180.54530.16310.9413-0.00490.0679-0.29930.0225-0.0037-0.02710.0336-0.10350.00870.07010.0041-0.00810.0538-0.0270.23926.472-12.36656.783
80.7360.208-0.00381.0506-0.04190.81260.03290.1019-0.0761-0.033-0.0442-0.00880.05350.0820.01130.0630.0276-0.01470.0342-0.01560.041947.229.34720.85
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 202
2X-RAY DIFFRACTION2B5 - 202
3X-RAY DIFFRACTION3C8 - 205
4X-RAY DIFFRACTION4D8 - 205
5X-RAY DIFFRACTION5E5 - 205
6X-RAY DIFFRACTION6F8 - 204
7X-RAY DIFFRACTION7G8 - 204
8X-RAY DIFFRACTION8H7 - 204

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