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- PDB-7la3: Pseudomonas fluorescens G150A isocyanide hydratase (G150A-3) at 2... -

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Basic information

Entry
Database: PDB / ID: 7la3
TitlePseudomonas fluorescens G150A isocyanide hydratase (G150A-3) at 274K, Refmac5-refined
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / DJ-1/PfpI superfamily
Function / homology: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / regulation of DNA-templated transcription / Isonitrile hydratase InhA
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.349 Å
AuthorsSu, Z. / Dasgupta, M. / Poitevin, F. / Mathews, I.I. / van den Bedem, H. / Wall, M.E. / Yoon, C.H. / Wilson, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139978 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123159 United States
CitationJournal: Struct Dyn. / Year: 2021
Title: Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.
Authors: Su, Z. / Dasgupta, M. / Poitevin, F. / Mathews, I.I. / van den Bedem, H. / Wall, M.E. / Yoon, C.H. / Wilson, M.A.
History
DepositionJan 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isonitrile hydratase InhA
B: Isonitrile hydratase InhA


Theoretical massNumber of molelcules
Total (without water)48,3892
Polymers48,3892
Non-polymers00
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-33 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.318, 58.245, 69.095
Angle α, β, γ (deg.)90.000, 112.744, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isonitrile hydratase InhA


Mass: 24194.674 Da / Num. of mol.: 2 / Mutation: G150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria)
Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: inhA, PFL_4109 / Plasmid: pet15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4K977
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 23% PEG 3350, 100MM TRIS-HCL PH 8.6, 200 MM MAGNESIUM CHLORIDE AND 2 MM DITHIOTHREITOL

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Data collection

DiffractionMean temperature: 274 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2018
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 1.349→39.17 Å / Num. obs: 85576 / % possible obs: 93 % / Redundancy: 2.1 % / CC1/2: 0.998 / Rrim(I) all: 0.064 / Net I/σ(I): 6
Reflection shellResolution: 1.349→1.38 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4083 / CC1/2: 0.264 / Rrim(I) all: 1.384 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NI5

6ni5


Resolution: 1.349→39.17 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 2.533 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.052
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1554 2602 3.065 %random
Rwork0.1201 82293 --
all0.121 ---
obs-84895 91.948 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.122 Å2
Baniso -1Baniso -2Baniso -3
1--0.249 Å20 Å2-0.18 Å2
2--0.261 Å20 Å2
3---0.103 Å2
Refinement stepCycle: LAST / Resolution: 1.349→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 0 323 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134536
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174330
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6436299
X-RAY DIFFRACTIONr_angle_other_deg1.4231.5739971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.00120.782243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20615696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2151544
X-RAY DIFFRACTIONr_chiral_restr0.0780.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025596
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021100
X-RAY DIFFRACTIONr_nbd_refined0.2210.2916
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.23520
X-RAY DIFFRACTIONr_nbtor_refined0.1570.22000
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1260.211
X-RAY DIFFRACTIONr_nbd_other0.1580.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.211
X-RAY DIFFRACTIONr_mcbond_it1.5371.5852361
X-RAY DIFFRACTIONr_mcbond_other1.5291.5822360
X-RAY DIFFRACTIONr_mcangle_it1.9522.3793058
X-RAY DIFFRACTIONr_mcangle_other1.9552.3813059
X-RAY DIFFRACTIONr_scbond_it2.1911.9922175
X-RAY DIFFRACTIONr_scbond_other2.1911.9942176
X-RAY DIFFRACTIONr_scangle_it2.7382.8523241
X-RAY DIFFRACTIONr_scangle_other2.7382.8543242
X-RAY DIFFRACTIONr_lrange_it3.10819.9144843
X-RAY DIFFRACTIONr_lrange_other3.02719.6314797
X-RAY DIFFRACTIONr_rigid_bond_restr1.5338866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.349-1.3840.3341760.2975658X-RAY DIFFRACTION85.6304
1.384-1.4220.3131910.2635893X-RAY DIFFRACTION92.6168
1.422-1.4630.2371910.2335855X-RAY DIFFRACTION93.6783
1.463-1.5080.2161830.1945718X-RAY DIFFRACTION93.7858
1.508-1.5580.2091530.1695258X-RAY DIFFRACTION89.6603
1.558-1.6120.1981690.1425246X-RAY DIFFRACTION91.9199
1.612-1.6730.181530.1275303X-RAY DIFFRACTION96.0056
1.673-1.7410.1581590.1025023X-RAY DIFFRACTION95.3099
1.741-1.8190.1521740.0964805X-RAY DIFFRACTION94.7479
1.819-1.9070.1371330.0864585X-RAY DIFFRACTION94.4923
1.907-2.0110.1291480.0824343X-RAY DIFFRACTION94.2497
2.011-2.1320.1331400.0893980X-RAY DIFFRACTION91.4539
2.132-2.2790.127970.0863486X-RAY DIFFRACTION84.2464
2.279-2.4620.1251340.0883605X-RAY DIFFRACTION94.5625
2.462-2.6960.1251040.13308X-RAY DIFFRACTION93.8394
2.696-3.0140.142880.1152988X-RAY DIFFRACTION92.4835
3.014-3.4790.147710.1192564X-RAY DIFFRACTION90.2706
3.479-4.2580.151470.1072012X-RAY DIFFRACTION83.1583
4.258-6.0080.143620.1181685X-RAY DIFFRACTION90.1445
6.008-39.170.13290.146978X-RAY DIFFRACTION90.5575

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