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- PDB-3ooq: CRYSTAL STRUCTURE OF amidohydrolase from Thermotoga maritima MSB8 -

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Basic information

Entry
Database: PDB / ID: 3ooq
TitleCRYSTAL STRUCTURE OF amidohydrolase from Thermotoga maritima MSB8
Componentsamidohydrolase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Similarity search - Function
Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel ...Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Amidohydro-rel domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF amidohydrolase from Thermotoga maritima MSB8
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: amidohydrolase
B: amidohydrolase
C: amidohydrolase
D: amidohydrolase
E: amidohydrolase
F: amidohydrolase
G: amidohydrolase
H: amidohydrolase
I: amidohydrolase
J: amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,27415
Polymers443,81410
Non-polymers4605
Water31,9231772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46840 Å2
ΔGint-188 kcal/mol
Surface area121620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.450, 148.300, 195.020
Angle α, β, γ (deg.)90.000, 105.310, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asymmetric unit

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Components

#1: Protein
amidohydrolase


Mass: 44381.352 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: AE001811_9, TM_1723 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q9X247
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1772 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Na-malonate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 495851 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Χ2: 0.963 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.06-2.13.40.771237040.79993
2.1-2.133.40.696238140.81193.5
2.13-2.173.50.615240210.81294.2
2.17-2.223.50.561241310.81294.8
2.22-2.273.50.497242050.81695.2
2.27-2.323.50.42243490.81495.6
2.32-2.383.50.382244220.81196.2
2.38-2.443.50.333245310.81596.6
2.44-2.513.50.285247620.82497.1
2.51-2.63.50.255248990.83297.6
2.6-2.693.50.226249130.84598
2.69-2.83.50.179251660.84598.6
2.8-2.923.60.155251240.85298.9
2.92-3.083.60.123252130.87399.2
3.08-3.273.60.09253690.91799.7
3.27-3.523.70.07254611.01499.7
3.52-3.883.70.059253971.33399.9
3.88-4.443.80.054255001.639100
4.44-5.593.80.043254681.22100
5.59-503.90.038254021.28499.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.06→19.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.1907 / WRfactor Rwork: 0.1505 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8808 / SU B: 9.182 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1855 / SU Rfree: 0.1627 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.213 12737 5 %RANDOM
Rwork0.1672 ---
obs0.1695 252990 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 72.73 Å2 / Biso mean: 28.849 Å2 / Biso min: 6.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.02 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.06→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29743 0 30 1772 31545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02230384
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.98541027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10953839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09624.3551240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.198155571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.34715170
X-RAY DIFFRACTIONr_chiral_restr0.0890.24674
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122418
X-RAY DIFFRACTIONr_mcbond_it0.8323.519066
X-RAY DIFFRACTIONr_mcangle_it3.2255030904
X-RAY DIFFRACTIONr_scbond_it8.045011318
X-RAY DIFFRACTIONr_scangle_it1.1674.510116
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 906 -
Rwork0.219 16770 -
all-17676 -
obs--94.03 %
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)
10.3153-0.1475-0.02370.43880.07290.1896-0.0014-0.05970.02820.02290.0116-0.0305-0.02880.0068-0.01020.0448-0.02280.01390.0241-0.01280.030334.1125110.05374.4181
20.40070.00040.15110.38190.16290.5592-0.0388-0.0630.0758-0.01890.00710.054-0.0836-0.13560.03160.01790.02210.00230.0405-0.00530.04230.1142109.642761.4186
30.30520.0129-0.05910.08570.04510.35620.0223-0.0278-0.03810.02590.0249-0.00820.0842-0.0088-0.04730.051-0.0114-0.01090.02070.01660.056727.031968.205284.3368
40.16340.0053-0.02020.2737-0.1170.57640.033-0.0161-0.01870.0174-0.00510.05360.072-0.1234-0.02780.0449-0.0523-0.00410.06940.01810.064-5.415966.812767.5342
50.3348-0.0667-0.05110.2651-0.04050.38840.01080.0767-0.0275-0.06790.01670.02790.03350.0379-0.02750.0456-0.04030.01050.0832-0.03430.019624.69676.66734.8062
60.23690.0236-0.06720.296-0.12290.1772-0.02210.04220.0278-0.00880.0366-0.0011-0.04860.0495-0.01450.0647-0.0730.00430.088-0.00070.027552.9944111.311234.9782
70.24970.16310.01780.3473-0.03020.303-0.04380.08480.0485-0.02010.02160.0361-0.10210.00060.02220.0871-0.041-0.02230.05590.03030.037118.759115.608122.6951
80.4237-0.06880.09930.4035-0.03110.26980.04290.0576-0.0949-0.01040.02060.01340.1358-0.0471-0.06350.1031-0.0447-0.0240.0392-0.02180.09249.793646.498532.3866
90.44680.09650.09730.25220.12480.42940.00250.1442-0.0615-0.02090.0297-0.0730.01890.1646-0.03220.011-0.00880.02150.1549-0.06240.059857.004970.63120.9136
100.42150.1450.06020.34620.07880.27140.05270.0238-0.1460.01620.0322-0.0640.15210.0876-0.08480.09510.0461-0.03940.0298-0.03620.106441.173343.893351.11
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 389
2X-RAY DIFFRACTION2B6 - 388
3X-RAY DIFFRACTION3C6 - 389
4X-RAY DIFFRACTION4D6 - 389
5X-RAY DIFFRACTION5E6 - 388
6X-RAY DIFFRACTION6F5 - 389
7X-RAY DIFFRACTION7G6 - 388
8X-RAY DIFFRACTION8H6 - 388
9X-RAY DIFFRACTION9I6 - 388
10X-RAY DIFFRACTION10J6 - 388

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