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- PDB-7jka: Dienelactone hydrolase family protein m3DLH from Halieaceae bacterium -

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Basic information

Entry
Database: PDB / ID: 7jka
TitleDienelactone hydrolase family protein m3DLH from Halieaceae bacterium
Componentsm3DLH protein
KeywordsHYDROLASE / dienelactonase / phosphotriesterase
Biological speciesHalieaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsSchnettler Fernandez, J.D.F. / Campbell, E.C. / Hollfelder, F.H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission695669European Union
CitationJournal: To Be Published
Title: m3DLH
Authors: Schnettler Fernandez, J.D.F. / Campbell, E.C. / Hollfelder, F.
History
DepositionJul 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.country
Revision 1.2Mar 12, 2025Group: Structure summary / Category: pdbx_entry_details / struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: m3DLH protein


Theoretical massNumber of molelcules
Total (without water)27,7801
Polymers27,7801
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.445, 43.680, 59.645
Angle α, β, γ (deg.)90.000, 92.713, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-420-

HOH

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Components

#1: Protein m3DLH protein


Mass: 27780.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halieaceae bacterium (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 36.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na3 Cit 5.6 pH (Buffer) 30 %w/v PEG 4K (Precipitant) 0.2 M NH4 Acet (Salt)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.53→24.27 Å / Num. obs: 29979 / % possible obs: 98.36 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1138 / Net I/σ(I): 9.53
Reflection shellResolution: 1.53→1.58 Å / Rmerge(I) obs: 0.5259 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 2912 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3f67

3f67


Resolution: 1.53→24.27 Å / SU ML: 0.1537 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7859
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2014 1475 4.93 %
Rwork0.1639 28474 -
obs0.1657 29949 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.52 Å2
Refinement stepCycle: LAST / Resolution: 1.53→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 205 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821991
X-RAY DIFFRACTIONf_angle_d0.97482710
X-RAY DIFFRACTIONf_chiral_restr0.0582280
X-RAY DIFFRACTIONf_plane_restr0.0055372
X-RAY DIFFRACTIONf_dihedral_angle_d23.9601727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.580.2431470.23132474X-RAY DIFFRACTION95.48
1.58-1.640.24251460.20212517X-RAY DIFFRACTION97.4
1.64-1.710.25071350.18762564X-RAY DIFFRACTION97.4
1.71-1.780.21011240.18292566X-RAY DIFFRACTION98.39
1.78-1.880.23331420.18042574X-RAY DIFFRACTION98.12
1.88-1.990.24461260.16552591X-RAY DIFFRACTION98.48
1.99-2.150.20161310.16082597X-RAY DIFFRACTION99.06
2.15-2.360.19091220.16212620X-RAY DIFFRACTION99.2
2.36-2.710.1741280.16512628X-RAY DIFFRACTION99.28
2.71-3.410.211520.1632615X-RAY DIFFRACTION99.6
3.41-24.270.17351220.14512728X-RAY DIFFRACTION99.89
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)
12.269653186820.08927165264520.2244168450356.640418879473.093656696473.94969699801-0.01377793350810.1605468876420.000798493834429-0.364435487458-0.1991548914830.268004214967-0.32073388838-0.2934310284010.2462913928750.145224733320.00508035793923-0.03038086714760.175884450010.008583889651530.147434972143-15.0861528949-15.28948357462.30107925602
22.38773759389-1.08424480783-0.008875125896793.02419074675-0.2120151876251.03500163693-0.1328561836920.03166352599350.379327295046-0.3026205028140.0749191513796-0.246104438944-0.3523771975460.06495314276550.01778146412960.237742562873-0.0387537303976-0.02596476178990.1214138150040.004476398237710.158439448274-6.27068619913-8.8274930909910.392184639
32.383552374310.06847401738990.3562410924122.629824963420.5931248562343.32885551061-0.0769540769777-0.130450553157-0.1428903519040.00730929368309-0.02590467768010.310130934201-0.0652372236355-0.3898809317630.1009309551380.09431464629850.01993855516880.008672521182120.139160795040.01180341573430.13298634536-17.4580724784-19.155009404111.7984488693
41.75564202138-1.33107067641-0.7226642637146.753716971550.2512377509696.02784353762-0.300472278687-0.214168354693-0.4537996498260.6259770128030.1896395780620.737837543150.304086437609-0.3924410865880.1560405989010.266479084897-0.03037086122530.04284106452710.1817460225270.02679470674850.253591993218-18.3736043043-36.85319664378.91812427049
50.6519300668880.1723049246910.4916116839091.194754312580.0686562099031.850540989470.0131479673470.0835367678203-0.031716843429-0.06337552203540.0831523633517-0.1015271411130.1264389654060.216533715828-0.08091860513670.08320506837730.003976913160280.01072441664360.113347669855-0.02414817135640.100613471304-3.49953114238-25.7618932519.36527474945
65.908314633591.18284663905-1.563975062743.53810113058-0.8429568632614.199847497310.05318529808560.0775162256208-0.568355334536-0.049401834123-0.01938514154840.01473025240150.416887695207-0.294981567817-0.06561549100360.169803133251-0.0318187810755-0.0271488387130.133112417791-0.008559743805410.146959169305-7.65191043059-30.997167103824.2418163679
77.55031774511-2.02469440473-1.224710159593.99828098051.579869831286.744735425010.215164572982-0.0658786961859-0.6663246862960.3135630460120.05352561879430.01647361056970.890452924070.293646954225-0.2232515241620.3217001720980.0814417253143-0.1010612691980.15846550915-0.04881948461340.1989286345921.29396345729-37.391515798121.193196119
81.287968407170.05836271765990.6734809427573.029202652060.1204819788143.351829513760.180207595587-0.052288535987-0.1559284127580.0183835801961-0.07440068489120.2891262878130.126736753629-0.201681715722-0.09559514893840.1352940392610.00536800015135-0.02337557584250.109211445595-0.01254536098280.0982680748592-7.49938643589-27.368945300525.049784288
92.81560218133-0.843887402471-0.7002389538443.17152474787-0.3485999500674.1709552929-0.09491491674190.0508439759587-0.1249108644360.04011270940960.1286131654350.3747520010330.106754947151-0.418916218534-0.01517390058860.1674460996790.00123896085002-0.0171271612840.167376422869-0.008174406238120.145060146028-10.1323893677-19.699365964725.2133458272
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 34 )14 - 343 - 24
22chain 'A' and (resid 35 through 48 )35 - 4825 - 40
33chain 'A' and (resid 49 through 86 )49 - 8641 - 81
44chain 'A' and (resid 87 through 100 )87 - 10082 - 95
55chain 'A' and (resid 101 through 171 )101 - 17196 - 169
66chain 'A' and (resid 172 through 185 )172 - 185170 - 183
77chain 'A' and (resid 186 through 198 )186 - 198184 - 196
88chain 'A' and (resid 199 through 221 )199 - 221197 - 219
99chain 'A' and (resid 222 through 250 )222 - 250220 - 249

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