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- PDB-8tt1: Pseudomonas fluorescens isocyanide hydratase pH=5.0 -

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Basic information

Entry
Database: PDB / ID: 8tt1
TitlePseudomonas fluorescens isocyanide hydratase pH=5.0
ComponentsIsonitrile hydratase InhA
KeywordsLYASE / isocyanide / isonitrile
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: 1.45 Å
AuthorsWilson, M.A. / Smith, N. / Dasgupta, M. / Dolamore, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139978 United States
Citation
Journal: Sci Adv / Year: 2024
Title: Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.
Authors: Smith, N. / Dasgupta, M. / Wych, D.C. / Dolamore, C. / Sierra, R.G. / Lisova, S. / Marchany-Rivera, D. / Cohen, A.E. / Boutet, S. / Hunter, M.S. / Kupitz, C. / Poitevin, F. / Moss 3rd, F.R. ...Authors: Smith, N. / Dasgupta, M. / Wych, D.C. / Dolamore, C. / Sierra, R.G. / Lisova, S. / Marchany-Rivera, D. / Cohen, A.E. / Boutet, S. / Hunter, M.S. / Kupitz, C. / Poitevin, F. / Moss 3rd, F.R. / Mittan-Moreau, D.W. / Brewster, A.S. / Sauter, N.K. / Young, I.D. / Wolff, A.M. / Tiwari, V.K. / Kumar, N. / Berkowitz, D.B. / Hadt, R.G. / Thompson, M.C. / Follmer, A.H. / Wall, M.E. / Wilson, M.A.
#1: Journal: Biorxiv / Year: 2023
Title: Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography.
Authors: Smith, N. / Dasgupta, M. / Wych, D.C. / Dolamore, C. / Sierra, R.G. / Lisova, S. / Marchany-Rivera, D. / Cohen, A.E. / Boutet, S. / Hunter, M.S. / Kupitz, C. / Poitevin, F. / Moss, F.R. / ...Authors: Smith, N. / Dasgupta, M. / Wych, D.C. / Dolamore, C. / Sierra, R.G. / Lisova, S. / Marchany-Rivera, D. / Cohen, A.E. / Boutet, S. / Hunter, M.S. / Kupitz, C. / Poitevin, F. / Moss, F.R. / Brewster, A.S. / Sauter, N.K. / Young, I.D. / Wolff, A.M. / Tiwari, V.K. / Kumar, N. / Berkowitz, D.B. / Hadt, R.G. / Thompson, M.C. / Follmer, A.H. / Wall, M.E. / Wilson, M.A.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionAug 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details

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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)48,3612
Polymers48,3612
Non-polymers00
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-29 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.051, 40.724, 83.430
Angle α, β, γ (deg.)90.000, 104.418, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Isonitrile hydratase InhA / isocyanide hydratase


Mass: 24180.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: inhA / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4K977
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.94 Å3/Da / Density % sol: 36.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 23% PEG 3350, 200 mM MgCl2, 2 mM DTT and 100mM sodium acetate pH=5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.886 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2019
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.45→37.34 Å / Num. obs: 65010 / % possible obs: 98.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.097 / Net I/σ(I): 10.1
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3157 / CC1/2: 0.427 / Rrim(I) all: 1.822 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoXDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→32.78 Å / SU ML: 0.1655 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1818 3233 4.98 %
Rwork0.1556 61687 -
obs0.1569 64920 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.5 Å2
Refinement stepCycle: LAST / Resolution: 1.45→32.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 0 429 3798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473667
X-RAY DIFFRACTIONf_angle_d0.74625040
X-RAY DIFFRACTIONf_chiral_restr0.07581
X-RAY DIFFRACTIONf_plane_restr0.0064682
X-RAY DIFFRACTIONf_dihedral_angle_d12.18781336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.34411520.3062569X-RAY DIFFRACTION96.32
1.47-1.490.28381420.2822698X-RAY DIFFRACTION97.93
1.49-1.520.26231270.25342639X-RAY DIFFRACTION97.88
1.52-1.550.2711610.23822656X-RAY DIFFRACTION98.36
1.55-1.570.23121230.22342692X-RAY DIFFRACTION98.32
1.57-1.60.22511390.21292657X-RAY DIFFRACTION98.14
1.6-1.640.24721340.22472636X-RAY DIFFRACTION96.48
1.64-1.670.28231350.21262648X-RAY DIFFRACTION97.65
1.67-1.710.2631280.19592704X-RAY DIFFRACTION98.68
1.71-1.750.2131350.1792680X-RAY DIFFRACTION98.5
1.75-1.80.21271650.16612661X-RAY DIFFRACTION98.64
1.8-1.850.21231360.15872709X-RAY DIFFRACTION98.51
1.85-1.910.1991490.15042646X-RAY DIFFRACTION98.59
1.91-1.980.1881300.14842619X-RAY DIFFRACTION95.55
1.98-2.060.16981100.13882749X-RAY DIFFRACTION98.76
2.06-2.160.15111370.1332699X-RAY DIFFRACTION99.09
2.16-2.270.15131420.13242703X-RAY DIFFRACTION98.61
2.27-2.410.17521570.13072685X-RAY DIFFRACTION98.92
2.41-2.60.18921510.13382650X-RAY DIFFRACTION96.45
2.6-2.860.15481390.14032727X-RAY DIFFRACTION99.2
2.86-3.270.17061480.14052731X-RAY DIFFRACTION99.45
3.27-4.120.14351480.13262712X-RAY DIFFRACTION97.05
4.12-32.780.16281450.15872817X-RAY DIFFRACTION98.5
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)
11.97491162814-0.4365633109790.5799776969130.982030089591-0.1358791329861.9419615953-0.0455007834756-0.101458471545-0.2789165380250.04638441013310.02698358751660.2537824776370.143276867632-0.2101879943310.02345486770750.112669326192-0.01892467602850.01721988259830.1270113183870.0157935246850.165199652028-9.3537120742-2.84980960958-22.140020853
27.012732522180.0481478505315-1.048586651584.13705134316-0.9303478133443.334651136360.005666331590010.2780463979220.448763351375-0.1341386798980.09321795135260.218678026552-0.182389281495-0.13012323668-0.03358174843770.1038860905710.00512176467939-0.04068144392070.1531987927820.0251248248980.152540649291-10.196048761311.7285239258-34.2489501615
31.46679638489-0.1676987557370.2820756432420.199667923759-0.005848389441631.83685894166-0.0101696637917-0.04692704648210.07016562327690.02397488504480.02265996057640.082051676723-0.140527941879-0.0707810953196-0.0194647599670.1763531910220.01155532594310.006256001685620.1337423308252.90021800756E-50.200143802812-1.2948213199412.3749000265-18.2075205227
49.216107502595.2619568278-0.4591283927913.8878047785-0.4338990915811.38998625129-0.4008541142160.484152024245-0.298890750572-0.6420440268580.148437753242-0.09057954836190.162457520060.03146922474030.2104925746130.2583487307630.00431037044217-0.03651848761910.228954714147-0.0207279332810.172897220261-3.991213873574.26834313703-43.4060550296
53.008108330660.0105847866402-1.030982035741.55708334326-0.49807815783.3438757398-0.04767466409990.110377747727-0.204372301997-0.04281521133270.0238544477857-0.01219221488740.1464646166190.01739593046390.02203498555020.0905693113932-0.00626851857892-0.02078427648970.099869149568-0.01926752633340.08906659158411.6941626667-6.47542075959-20.8804305974
61.679824273830.2597452155990.3999821327011.146619718590.1170665087250.712123977050.01988966293820.0222952611437-0.2878787439150.0411517446845-0.0190423565304-0.1125377400340.2167673846450.02755322949410.01371597351770.1507310277550.0163699961203-0.01375792380690.1313015179490.01560458077230.16412030995818.6914567921-9.04729603938-14.5569822932
76.157895048062.37050953155-2.648271459238.25305208587-6.420465020188.223759198490.02514269539390.158613519863-0.530221332096-0.219618702652-0.226062784581-0.5158769110410.5416434709980.3920858001130.2346522884060.1550274771220.045355719348-0.03421495306760.173271219107-0.007076081139140.17372368453126.4904612322-8.78045656865-15.4485962299
81.70118803520.09009276676430.9275847593921.062722619470.3823578780033.62947044819-0.0444817074773-0.01580614048060.0755085226394-0.0003763608406660.0120933236263-0.00320601908604-0.1683309616280.08896562146680.03198018786160.105656951798-0.0134779644104-0.005809267252880.1052785036620.006908898696980.11293428428520.90346871276.37691827863-12.2930138996
98.82399258945-4.645946404921.079052885953.36790978454-1.539783655791.176658191110.2093861840550.787601706949-0.340961014959-0.2766762869-0.1902890365210.0297906629159-0.01435652903770.30090456592-0.04122971148780.1595952229140.001404643539420.003942688886820.2979537409620.02798964280080.14741880490613.08168727938.26333921356-34.9776425155
101.81327363252-0.5243618082722.153819125981.121780082210.2642567592846.27773048583-0.187274930677-0.1951916286580.2002925071390.09410001811850.0671253519964-0.0240115443411-0.37778579451-0.1891959376230.1071635779790.1012036007670.01273989234350.01739417950670.1375635943730.004101765034310.1843253687454.231127864214.4897720925-7.4077791468
115.07646889227-4.71282660266-2.553193662044.36126855092.339283220011.989385239120.00267889549041-0.2167066113910.04053452686640.218203962908-0.04929440180650.02041777052330.02690564831850.09883482608740.04405506187380.2105330691040.01878809286830.003571197496180.2549439136620.05322554374670.14941621124720.0261925298-1.685780308753.67773972042
122.127665756582.022174387762.121166767642.112034668261.867965367532.22989542196-6.72935972244-5.80713926047-8.0498968544112.34291898153.683836948851.466654931824.092937463856.040113058193.038364616760.943943264166-0.02437434753080.282763035150.5436966295130.01603352186550.90761380475335.8507568526-7.026942211040.516168000318
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 109 )AA2 - 1091 - 108
22chain 'A' and (resid 110 through 139 )AA110 - 139109 - 138
33chain 'A' and (resid 140 through 196 )AA140 - 196139 - 195
44chain 'A' and (resid 197 through 227 )AA197 - 227196 - 226
55chain 'B' and (resid -1 through 53 )BB-1 - 531 - 55
66chain 'B' and (resid 54 through 80 )BB54 - 8056 - 82
77chain 'B' and (resid 81 through 95 )BB81 - 9583 - 97
88chain 'B' and (resid 96 through 166 )BB96 - 16698 - 168
99chain 'B' and (resid 167 through 178 )BB167 - 178169 - 180
1010chain 'B' and (resid 179 through 207 )BB179 - 207181 - 209
1111chain 'B' and (resid 208 through 226 )BB208 - 226210 - 228
1212chain 'B' and (resid 227 through 227 )BB227229

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