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- PDB-2v7g: Crystal Structure of an Engineered Urocanase Tetramer -

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Basic information

Entry
Database: PDB / ID: 2v7g
TitleCrystal Structure of an Engineered Urocanase Tetramer
ComponentsUROCANATE HYDRATASE
KeywordsLYASE / HISTIDINE DEGRADATION / NAD / PROTEIN ENGINEERING / UROCANATE HYDRATASE / HISTIDINE METABOLISM
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 fold / Urocanase superfamily / Urocanase like domains / : / Urocanase conserved site / Urocanase signature. / Urocanase / Urocanase, Rossmann-like domain / Urocanase, N-terminal domain / Urocanase, C-terminal domain ...Urocanase fold / Urocanase superfamily / Urocanase like domains / : / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Urocanate hydratase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTreiber, N. / Schulz, G.E.
CitationJournal: Science / Year: 2008
Title: Designed Protein-Protein Association.
Authors: Grueninger, D. / Treiber, N. / Ziegler, M.O.P. / Koetter, J.W.A. / Schulze, M.-S. / Schulz, G.E.
History
DepositionJul 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UROCANATE HYDRATASE
B: UROCANATE HYDRATASE
C: UROCANATE HYDRATASE
D: UROCANATE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,14324
Polymers243,2474
Non-polymers3,89620
Water23,6001310
1
A: UROCANATE HYDRATASE
C: UROCANATE HYDRATASE
hetero molecules

B: UROCANATE HYDRATASE
D: UROCANATE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,14324
Polymers243,2474
Non-polymers3,89620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
2
B: UROCANATE HYDRATASE
D: UROCANATE HYDRATASE
hetero molecules

A: UROCANATE HYDRATASE
C: UROCANATE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,14324
Polymers243,2474
Non-polymers3,89620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
3
A: UROCANATE HYDRATASE
C: UROCANATE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,37110
Polymers121,6232
Non-polymers1,7478
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-58.4 kcal/mol
Surface area41470 Å2
MethodPQS
4
B: UROCANATE HYDRATASE
D: UROCANATE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,77214
Polymers121,6232
Non-polymers2,14912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-55.4 kcal/mol
Surface area41310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)68.068, 154.316, 216.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.073347, -0.612583, -0.786996), (-0.625688, 0.642766, -0.442003), (0.776618, 0.459994, -0.430431)-14.7541, 19.6974, -66.6333
2given(-0.065725, -0.614523, -0.786156), (-0.620006, 0.642465, -0.450368), (0.78184, 0.457821, -0.423234)-15.0703, 19.528, -66.5006

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Components

#1: Protein
UROCANATE HYDRATASE / UROCANASE / IMIDAZOLONEPROPIONATE HYDROLASE


Mass: 60811.684 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25080, urocanate hydratase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1310 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CONFLICTS ANNOTATED BELOW IN THE SEQADV RECORDS BELOW CORRESPOND TO A KNOWN CONFLICT ...THE SEQUENCE CONFLICTS ANNOTATED BELOW IN THE SEQADV RECORDS BELOW CORRESPOND TO A KNOWN CONFLICT IN THE UNIPROT SEQUENCE DATABASE ENTRY FOR P25080 (TVKA->SLKG) AT POSITIONS 164-167 OF THE SEQUENCE DATABASE ENTRY. THIS CONFLICT HAS BEEN DESCRIBED BY S.L.ALLISION AND A.T.PHILLIPS IN 1993.

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6.6
Details: 10% (W/V) PEG8000, 0.2 M MGAC2, 20% (V/V) GLYCERIN, 0.1 M NA CACODYLATE PH 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8853
DetectorType: MARREASEARCH / Detector: CCD / Date: Nov 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8853 Å / Relative weight: 1
ReflectionResolution: 2→28.8 Å / Num. obs: 149793 / % possible obs: 97 % / Observed criterion σ(I): 6.6 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.06 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 6.6 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UWL

1uwl


Resolution: 2→28.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.721 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1498 1 %RANDOM
Rwork0.156 ---
obs0.156 148293 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.01 Å2
Refinement stepCycle: LAST / Resolution: 2→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16960 0 258 1310 18528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02217590
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.96423882
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84152208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00723.838792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.636152808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.10915132
X-RAY DIFFRACTIONr_chiral_restr0.0810.22596
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213484
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.29154
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.211957
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.21335
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4471.511297
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.684217450
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28937315
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.034.56432
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.24 100
Rwork0.173 9965
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)
10.549-0.25440.18250.9043-0.15140.5967-0.04220.02550.0840.08090.0087-0.0447-0.11410.01390.0335-0.1149-0.0187-0.0065-0.1406-0.0036-0.1387-22.505529.0837-52.3957
20.6254-0.1786-0.01630.8517-0.13160.78270.01580.04690.0338-0.0527-0.01880.0121-0.12730.01980.0031-0.1151-0.0317-0.0054-0.13130.0137-0.1485.746317.3238-4.1693
30.31820.19950.16480.94150.40460.55930.03940.0569-0.09240.03010.029-0.11650.13480.091-0.0684-0.09160.0206-0.0263-0.0875-0.0097-0.0787-11.9008-10.125-57.3232
40.1166-0.07940.1060.8611-0.54431.1020.01480.0197-0.0627-0.0819-0.0947-0.15610.19210.20810.0798-0.09920.03320.0184-0.02240.0024-0.031925.3439-16.80966.975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 557
2X-RAY DIFFRACTION2B5 - 557
3X-RAY DIFFRACTION3C5 - 557
4X-RAY DIFFRACTION4D5 - 557

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