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- PDB-4dw8: Crystal structure of a haloacid dehalogenase-like hydrolase (Targ... -

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Basic information

Entry
Database: PDB / ID: 4dw8
TitleCrystal structure of a haloacid dehalogenase-like hydrolase (Target EFI-900331) from Bacteroides thetaiotaomicron with bound Na crystal form I
ComponentsHaloacid dehalogenase-like hydrolase
KeywordsHYDROLASE / HAD / putative phosphatase / Enzyme Function Initiative / EFI / Structural Genomics
Function / homology
Function and homology information


phosphatase activity / magnesium ion binding / cytosol
Similarity search - Function
Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Hypothetical cof family signature 2. / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Hypothetical cof family signature 2. / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Haloacid dehalogenase-like hydrolase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsVetting, M.W. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Allen, K.N. / Dunaway-Mariano, D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a haloacid dehalogenase-like hydrolase (Target EFI-900331) from Bacteroides thetaiotaomicron with bound Na crystal form I
Authors: Vetting, M.W. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Allen, K.N. / Dunaway-Mariano, D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionFeb 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _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: Haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2245
Polymers31,2011
Non-polymers234
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.669, 73.133, 82.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloacid dehalogenase-like hydrolase


Mass: 31200.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3352 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8A2F3, Hydrolases; Acting on halide bonds; In carbon-halide compounds
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.75
Details: protein solution: 10 mM HEPES, pH 7.8, 150 mM sodium chloride, 10% glycerol, 5 mM magnesium, reservoir solution: 20% PEG4000, 100 mM sodium acetate, pH 4.75, 200 mM ammonium acetate, 12% ...Details: protein solution: 10 mM HEPES, pH 7.8, 150 mM sodium chloride, 10% glycerol, 5 mM magnesium, reservoir solution: 20% PEG4000, 100 mM sodium acetate, pH 4.75, 200 mM ammonium acetate, 12% ethylene glycol, cryoprotectant: reservoir solution + 10% glycerol + 10% ethylene glycol + 200 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 1, 2011 / Details: mirrors
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 42541 / Num. obs: 42541 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Χ2: 1.137 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.536.20.44920771.043199.4
1.53-1.556.20.39221321.034199.4
1.55-1.586.20.33120721.061199.4
1.58-1.626.20.28721181.058199.5
1.62-1.656.20.23320871.066199.7
1.65-1.696.20.20421301.047199.4
1.69-1.736.20.17121041.051199.8
1.73-1.786.20.14121151.02199.4
1.78-1.836.20.12321181.036199.6
1.83-1.896.20.10321311.057199.6
1.89-1.966.40.10221001.303199.7
1.96-2.046.50.10521561.249199.8
2.04-2.136.60.11521261.2851100
2.13-2.246.80.11421511.4311100
2.24-2.3870.11221421.4661100
2.38-2.567.20.08921731.0291100
2.56-2.827.30.05221741.1231100
2.82-3.237.30.03921771.2321100
3.23-4.0770.0321941.02198.7
4.07-4060.02520641.038188

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NIW

3niw


Resolution: 1.502→20.281 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8756 / SU ML: 0.12 / σ(F): 0 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1906 4.67 %RANDOM
Rwork0.181 ---
all0.1824 40830 --
obs0.1824 40830 95.1 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.686 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 56.72 Å2 / Biso mean: 23.8647 Å2 / Biso min: 10.64 Å2
Baniso -1Baniso -2Baniso -3
1-4.9275 Å2-0 Å2-0 Å2
2---2.059 Å2-0 Å2
3----2.8684 Å2
Refinement stepCycle: LAST / Resolution: 1.502→20.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 4 232 2313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132193
X-RAY DIFFRACTIONf_angle_d1.4552987
X-RAY DIFFRACTIONf_chiral_restr0.1347
X-RAY DIFFRACTIONf_plane_restr0.007388
X-RAY DIFFRACTIONf_dihedral_angle_d11.848840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.502-1.53930.24131260.21242515264188
1.5393-1.58090.24841290.2042632276191
1.5809-1.62740.23181230.18722648277192
1.6274-1.67990.20721360.1792672280893
1.6799-1.740.20621370.16792715285294
1.74-1.80960.18781310.16972705283694
1.8096-1.89190.21161340.16732757289195
1.8919-1.99150.2081380.1752835297397
1.9915-2.11620.20551410.17792881302299
2.1162-2.27940.18231420.17282900304299
2.2794-2.50840.20961430.18432912305599
2.5084-2.87050.19561430.19312922306599
2.8705-3.61320.24281440.182429733117100
3.6132-20.28290.20491390.17892857299691
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)
14.24460.01620.90763.95120.93093.84670.05050.3724-0.1197-0.26650.05480.19110.25680.206-0.07110.19910.0168-0.00520.15070.0070.116-14.4544-19.1511-30.1096
21.43110.02840.5061.3868-1.09463.19720.16380.15710.0402-0.1384-0.0462-0.17080.06860.5348-0.11590.12090.02580.00780.1846-0.02820.1384-4.4262-21.4944-17.8543
31.89970.5638-0.36523.62530.67442.31970.0941-0.1874-0.00150.1989-0.14250.05730.14120.03730.04860.07810.0017-0.02760.11270.00140.1036-13.4325-31.654-2.8635
41.93180.7065-0.28862.7536-2.49985.148-0.09580.09040.39230.2503-0.0891-0.2535-0.80480.30640.03650.1746-0.0474-0.04660.154-0.01050.2545-6.7799-8.4382-15.8642
52.8162-1.10351.19043.95010.61783.3696-0.0885-0.136-0.01030.2330.04410.2090.0848-0.19690.03830.16470.00830.01130.11430.0190.1462-21.7225-11.4096-24.159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:35)A2 - 35
2X-RAY DIFFRACTION2(chain A and resid 36:95)A36 - 95
3X-RAY DIFFRACTION3(chain A and resid 96:190)A96 - 190
4X-RAY DIFFRACTION4(chain A and resid 191:214)A191 - 214
5X-RAY DIFFRACTION5(chain A and resid 215:267)A215 - 267

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