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- PDB-3h3e: Crystal structure of Tm1679, A METAL-DEPENDENT HYDROLASE OF THE B... -

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Basic information

Entry
Database: PDB / ID: 3h3e
TitleCrystal structure of Tm1679, A METAL-DEPENDENT HYDROLASE OF THE BETA-LACTAMASE SUPERFAMILY
Componentsuncharacterized protein Tm1679
Keywordsstructural genomics / METAL BINDING PROTEIN / Surface Entropy Reduction / ISFI / BETA-LACTAMASE SUPERFAMILY / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / unknown function
Function / homology
Function and homology information


transferase activity / metal ion binding
Similarity search - Function
Methanocaldococcus jannaschii dihydropteroate synthase-like, MBL-fold metallo hydrolase domain / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.749 Å
AuthorsCooper, D.R. / Olekhnovitch, N. / Derewenda, U. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: To be Published
Title: Crystal structure of Tm1679, A METAL-DEPENDENT HYDROLASE OF THE BETA-LACTAMASE SUPERFAMILY
Authors: Cooper, D.R. / Olekhnovitch, N. / Derewenda, Z.S.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein Tm1679
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5522
Polymers30,4871
Non-polymers651
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.169, 127.169, 41.044
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein uncharacterized protein Tm1679


Mass: 30486.984 Da / Num. of mol.: 1 / Mutation: K100Y, K101Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1679 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X207
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: Crystallization drop was 1:1 mixture of protein and 12% PEG 3000, 100 mM Sodium Citrate pH 5.3. The crystallization reservoir was 60 ul of 1.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 13.4 % / Number: 135066 / Rmerge(I) obs: 0.169 / Χ2: 1.31 / D res high: 2.75 Å / D res low: 30 Å / Num. obs: 10088 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.913098.710.0931.94514.4
4.75.9199.210.1221.61314.9
4.114.799.610.1121.57515.1
3.734.1199.510.1381.30615
3.463.7399.710.1891.16815
3.263.4699.610.2341.07914.9
3.13.2699.810.3271.03714.4
2.963.199.910.4281.03713
2.852.9699.810.5070.95710
2.752.8598.510.5640.9897.2
ReflectionResolution: 2.749→30 Å / Num. obs: 10088 / % possible obs: 99.4 % / Redundancy: 13.4 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 18.18
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.1 / % possible all: 98.5

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se53.4660.4970.6330.9950.998
2Se25.4850.5570.7360.80.655
3Se35.990.5990.7660.7180.761
4Se600.5430.6910.9720.759
5Se45.4060.4570.5830.4870.39
Phasing dmFOM : 0.68 / FOM acentric: 0.68 / FOM centric: 0.71 / Reflection: 9215 / Reflection acentric: 8406 / Reflection centric: 809
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.9-29.2260.860.90.73448343105
4.9-7.90.810.820.7513251162163
3.9-4.90.850.860.7716641505159
3.4-3.90.780.780.7115861473113
2.9-3.40.610.60.7227102526184
2.8-2.90.370.360.491482139785

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Processing

Software
NameVersionClassificationNB
SOLVE2.13phasing
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.749→29.226 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Stereochemistry target values: ML / Details: TLS refinement included
RfactorNum. reflection% reflection
Rfree0.207 281 1.47 %
Rwork0.151 --
obs0.151 19063 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.817 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 413.68 Å2 / Biso mean: 32.341 Å2 / Biso min: 6.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.633 Å20 Å2-0 Å2
2--0.633 Å20 Å2
3----1.266 Å2
Refinement stepCycle: LAST / Resolution: 2.749→29.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 1 89 2123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082072
X-RAY DIFFRACTIONf_angle_d1.0972784
X-RAY DIFFRACTIONf_chiral_restr0.071306
X-RAY DIFFRACTIONf_plane_restr0.004360
X-RAY DIFFRACTIONf_dihedral_angle_d16.677761
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.749-3.4630.2171410.1729340948198
3.463-29.2280.2011400.1399442958299
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)
10.8927-1.0141-0.08121.49530.24651.00970.0924-0.0120.1303-0.0146-0.0001-0.1335-0.05830.1352-0.0910.04810.00860.02240.0953-0.00660.102921.800868.582427.18
20000000000000000.44670.1274-0.05550.34520.01160.349721.311163.895619.8618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0 - 255
2X-RAY DIFFRACTION2chain ZA1 - 256

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