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Basic information

Entry
Database: PDB / ID: 4rpc
TitleCrystal structure of the putative alpha/beta hydrolase family protein from Desulfitobacterium hafniense
Componentsputative alpha/beta hydrolase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / AB hydrolase-1 domain-containing protein
Function and homology information
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the putative alpha/beta hydrolase family protein from Desulfitobacterium hafniense
Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative alpha/beta hydrolase
B: putative alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1384
Polymers59,8222
Non-polymers3162
Water4,197233
1
A: putative alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2273
Polymers29,9111
Non-polymers3162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)29,9111
Polymers29,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.661, 45.473, 82.787
Angle α, β, γ (deg.)90.00, 90.56, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.931942, -0.25814, 0.254652), (0.261715, 0.007228, 0.965118), (-0.250976, 0.96608, 0.060823)49.14965, -26.30386, 67.89312

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Components

#1: Protein putative alpha/beta hydrolase


Mass: 29910.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / Gene: Dhaf_3963 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) magic / References: UniProt: B8FSW0
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Bis-Tris, 25 % PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2014 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 27123 / Num. obs: 27123 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 24.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 93.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.071 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24684 1362 5 %RANDOM
Rwork0.17644 ---
obs0.18011 25718 99.18 %-
all-25718 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å2-0 Å2-0.38 Å2
2---0.83 Å2-0 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 15 233 4184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194027
X-RAY DIFFRACTIONr_bond_other_d0.0010.023948
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9935442
X-RAY DIFFRACTIONr_angle_other_deg0.85439068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77423.83188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39215660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5581530
X-RAY DIFFRACTIONr_chiral_restr0.0940.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02900
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4642.0571999
X-RAY DIFFRACTIONr_mcbond_other1.4622.0551997
X-RAY DIFFRACTIONr_mcangle_it2.2683.0762494
X-RAY DIFFRACTIONr_mcangle_other2.2683.0782495
X-RAY DIFFRACTIONr_scbond_it2.3422.4742028
X-RAY DIFFRACTIONr_scbond_other2.3362.4742028
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7013.5662949
X-RAY DIFFRACTIONr_long_range_B_refined6.26517.7374682
X-RAY DIFFRACTIONr_long_range_B_other6.26517.7424683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.097→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 85 -
Rwork0.242 1755 -
obs--91.5 %
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)
16.4564-0.6839-5.10270.9165-0.20556.0534-0.2859-0.1503-0.40880.1055-0.02420.13870.49570.1040.31010.1721-0.0040.02720.00770.00110.044611.114525.46177.3079
22.489-0.3245-1.24321.0632-0.44752.29470.0002-0.0579-0.1398-0.0591-0.01260.11130.2079-0.03680.01240.1624-0.01820.00480.017-0.00210.01810.668728.141773.0672
38.2411.0116-1.6011.8671-0.62624.99860.06720.26290.093-0.15440.0890.1954-0.2487-0.2843-0.15620.11370.01690.0290.02360.0080.07537.881939.018871.0513
42.0363-0.0081-1.05650.75570.07921.82220.1247-0.1750.1993-0.0002-0.0088-0.0447-0.03920.304-0.11590.16020.01320.01540.0539-0.01750.022225.538936.041867.4474
54.4216-0.1665-0.05841.9848-0.68482.63730.2767-0.36440.49710.2761-0.2024-0.0017-0.35480.2654-0.07430.2384-0.06130.04560.1092-0.06810.068717.330943.164679.764
61.8905-0.55530.49915.86490.51061.5806-0.12760.29540.3213-0.28690.0607-0.5306-0.10550.13950.06690.1028-0.00580.0180.08720.03540.095245.508217.214941.3656
71.24352.6727-0.19429.3588-4.53814.7832-0.12410.0756-0.1046-0.25490.2142-0.20040.0427-0.0944-0.09010.0870.04630.02850.10180.0440.150957.426514.007538.455
82.8860.7413-0.4973.5932-1.00021.1865-0.3214-0.20980.27830.2660.1052-0.71040.08370.08780.21620.09250.0539-0.1030.0602-0.05150.211252.733613.377552.142
91.4166-0.5769-0.23862.27530.50111.1003-0.19970.0037-0.04590.33320.02260.05670.2077-0.09760.17710.17780.05330.00710.0722-0.02890.03538.21436.44754.0266
102.9484-2.5358-0.32623.52740.73560.9062-0.3093-0.250.34580.70740.413-0.55680.01410.0544-0.10370.22950.1078-0.13630.1165-0.09360.105144.907420.097859.4872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 33
2X-RAY DIFFRACTION2A34 - 101
3X-RAY DIFFRACTION3A102 - 121
4X-RAY DIFFRACTION4A122 - 209
5X-RAY DIFFRACTION5A210 - 258
6X-RAY DIFFRACTION6B9 - 70
7X-RAY DIFFRACTION7B71 - 83
8X-RAY DIFFRACTION8B84 - 125
9X-RAY DIFFRACTION9B126 - 209
10X-RAY DIFFRACTION10B210 - 258

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