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- PDB-7jfz: Structure of Urocanate hydratase from Legionella pneumophila boun... -

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Basic information

Entry
Database: PDB / ID: 7jfz
TitleStructure of Urocanate hydratase from Legionella pneumophila bound to NAD
ComponentsUrocanate hydratase
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


urocanate hydratase / urocanate hydratase activity / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / cytoplasm
Similarity search - Function
Urocanase conserved site / Urocanase signature. / Urocanase / Urocanase, Rossmann-like domain / Urocanase, N-terminal domain / Urocanase, C-terminal domain / Urocanase superfamily / Urocanase, central domain superfamily / Urocanase Rossmann-like domain / Urocanase N-terminal domain / Urocanase C-terminal domain
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / SUCCINIC ACID / Urocanate hydratase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Structure of Urocanate hydratase from Legionella pneumophila bound to NAD
Authors: Delker, S.L. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3298
Polymers62,2371
Non-polymers1,0927
Water10,178565
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.190, 125.120, 142.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1297-

HOH

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Components

#1: Protein Urocanate hydratase / Urocanase / Imidazolonepropionate hydrolase


Mass: 62236.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: hutU, lpg1379 / Variant: DSM 7513 / Plasmid: LepnA.19522.a.B1.PW38395 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZVR1, urocanate hydratase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.96 % / Description: monomer
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: JCSG+ screen: 15% PEG 3350, 100mM succinic acid / NaOH pH 7.0. LepnA.19522.a.B1.PW38395 at 25.57mg/ml, 1 hr. soak with 5mM histidine; cryo: 25% ethylene glycol; tray 297183; puck bbh6-11

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 20, 2019
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→37.91 Å / Num. obs: 71884 / % possible obs: 99.9 % / Redundancy: 18.046 % / Biso Wilson estimate: 30.248 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.043 / Χ2: 1.073 / Net I/σ(I): 39.25 / Num. measured all: 1297200 / Scaling rejects: 1559
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.748.5270.5933.2444921527552680.9120.63299.9
1.74-1.7911.3270.4864.7157970512151180.9580.5199.9
1.79-1.8411.8390.3686.2858921498149770.9780.38599.9
1.84-1.912.3830.2917.9160292487548690.9870.30499.9
1.9-1.9612.9290.21910.8160664469646920.9920.22899.9
1.96-2.0313.5070.16414.2361779457445740.9960.17100
2.03-2.1114.1270.12419.8861961438643860.9970.129100
2.11-2.1916.8860.09628.1371901425942580.9990.099100
2.19-2.2918.6140.08334.7675592406840610.9990.08699.8
2.29-2.419.7440.07140.876842389538920.9990.07399.9
2.4-2.5320.9790.0647.7177812371137090.9990.06299.9
2.53-2.6922.7310.05555.5801483531352610.05699.9
2.69-2.8726.4720.05165.84873063303329810.05299.8
2.87-3.128.5230.04476.84876513076307310.04599.9
3.1-3.428.0840.03888.77807692876287610.038100
3.4-3.827.3640.033101.39712562604260410.033100
3.8-4.3927.2220.029109.8621212284228210.0399.9
4.39-5.3827.1760.028112.92535361973197010.02899.8
5.38-7.627.6870.028107.83429151550155010.029100
7.6-37.9125.3530.024113.82228439139010.9990.02598.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal apo structure

Resolution: 1.7→37.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1779 1957 2.83 %
Rwork0.1551 67296 -
obs0.1557 69253 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.74 Å2 / Biso mean: 25.9242 Å2 / Biso min: 10.52 Å2
Refinement stepCycle: final / Resolution: 1.7→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 76 577 4880
Biso mean--25.4 35.99 -
Num. residues----547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.740.30961090.25024177428685
1.74-1.790.23581400.21144373451389
1.79-1.840.22681470.19544475462291
1.84-1.90.20021270.18714606473393
1.9-1.970.22481770.17734693487095
1.97-2.050.19051560.16224808496498
2.05-2.140.16251250.15314939506499
2.14-2.250.19841140.153649755089100
2.25-2.40.20041510.153849365087100
2.4-2.580.17611280.158150205148100
2.58-2.840.1941220.161950085130100
2.84-3.250.18161730.155549855158100
3.25-4.10.14911580.143350575215100
4.1-37.910.15181300.136652445374100
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)
11.2693-0.1422-0.45911.42260.05142.0050.0372-0.02650.0999-0.0456-0.0377-0.3454-0.08980.4878-0.00660.1217-0.0019-0.02710.26560.01510.219317.118116.318137.1532
21.57130.6063-0.82942.6651-1.04721.9405-0.0109-0.0026-0.1227-0.306-0.1674-0.25930.30770.32010.13050.17820.03630.0410.19550.01820.138822.313232.08424.047
30.60390.2386-0.28892.0373-0.78050.68150.0763-0.02750.17610.1787-0.03190.0613-0.11380.0996-0.04020.1297-0.01720.0210.1756-0.03050.137712.460938.730114.1641
40.9366-0.1652-0.24321.0787-0.08261.7067-0.00080.0788-0.0329-0.2374-0.0299-0.12330.15320.11310.01470.16710.0120.00660.11010.00240.13637.278712.062519.0189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 147 )A17 - 147
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 271 )A148 - 271
3X-RAY DIFFRACTION3chain 'A' and (resid 272 through 376 )A272 - 376
4X-RAY DIFFRACTION4chain 'A' and (resid 377 through 563 )A377 - 563

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