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- PDB-3qnm: Haloalkane Dehalogenase Family Member from Bacteroides thetaiotao... -

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Basic information

Entry
Database: PDB / ID: 3qnm
TitleHaloalkane Dehalogenase Family Member from Bacteroides thetaiotaomicron of Unknown Function
ComponentsHaloacid dehalogenase-like hydrolase
KeywordsStructural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
HAD-superfamily hydrolase, subfamily IA, YjjG/PynA / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...HAD-superfamily hydrolase, subfamily IA, YjjG/PynA / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Haloacid dehalogenase-like hydrolase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMatthew, M.W. / Ramagopal, U.A. / Toro, R. / Dickey, M. / Sauder, J.M. / Poulter, C.D. / Burley, S.K. / Gerlt, J.A. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Haloalkane Dehalogenase Family Member from Bacteroides thetaiotaomicron of Unknown Function
Authors: Matthew, M.W. / Ramagopal, U.A. / Toro, R. / Dickey, M. / Sauder, J.M. / Poulter, C.D. / Burley, S.K. / Gerlt, J.A. / Almo, S.C.
History
DepositionFeb 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)28,9184
Polymers28,8231
Non-polymers953
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.850, 51.190, 123.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloacid dehalogenase-like hydrolase


Mass: 28822.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2271 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A5G8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein 12.35 mg/m, 10 mM HEPES pH 7.5, 150 mM NaCl, 10% glycerol, 5 mM DTT Precipitant, 100 mM Bis-Tris pH 6.5, 25% PEG 3350, 200 mM Magnesium Chloride hexahydrate, VAPOR DIFFUSION, SITTING ...Details: Protein 12.35 mg/m, 10 mM HEPES pH 7.5, 150 mM NaCl, 10% glycerol, 5 mM DTT Precipitant, 100 mM Bis-Tris pH 6.5, 25% PEG 3350, 200 mM Magnesium Chloride hexahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 29690 / Num. obs: 29690 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 18.84 Å2 / Rsym value: 0.77 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 3872 / Rsym value: 0.477 / % possible all: 88.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→35.159 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 17.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1490 5.08 %Random 5%
Rwork0.1664 ---
all0.1681 29310 --
obs0.1681 29310 95.8 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.076 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9362 Å20 Å20 Å2
2--2.4329 Å20 Å2
3----0.4967 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 3 226 2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112017
X-RAY DIFFRACTIONf_angle_d1.2272727
X-RAY DIFFRACTIONf_dihedral_angle_d13.625746
X-RAY DIFFRACTIONf_chiral_restr0.09279
X-RAY DIFFRACTIONf_plane_restr0.005354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.76080.24411280.21472326X-RAY DIFFRACTION81
1.7608-1.83130.24871300.20642580X-RAY DIFFRACTION91
1.8313-1.91460.21831270.17422724X-RAY DIFFRACTION94
1.9146-2.01550.22091550.16042754X-RAY DIFFRACTION96
2.0155-2.14180.21961690.16022817X-RAY DIFFRACTION98
2.1418-2.30710.20321510.15532842X-RAY DIFFRACTION99
2.3071-2.53930.18131500.15912855X-RAY DIFFRACTION99
2.5393-2.90650.21871690.17242898X-RAY DIFFRACTION99
2.9065-3.66130.1811530.16622949X-RAY DIFFRACTION100
3.6613-35.16620.18941580.16133075X-RAY DIFFRACTION99
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)
10.4885-0.3617-0.15180.42210.00580.63670.0133-0.05130.1168-0.0198-0.02130.00080.0424-0.21850.02620.1042-0.0055-0.00480.10230.01570.115241.124934.748679.3244
21.79680.1514-0.21441.17260.19181.2903-0.03910.0903-0.10190.12150.00910.06230.1659-0.06050.02870.1184-0.00620.01450.14950.00270.103121.226424.161967.6798
30.51010.0655-0.21390.13790.03750.5002-0.0320.23320.0026-0.0141-0.0110.0580.0256-0.0060.02950.1153-0.0057-0.00270.15050.01020.095545.096231.866374.3051
40.46170.1155-0.35350.59090.27711.39070.02250.05130.05320.0314-0.02310.0261-0.0354-0.0538-0.00390.0990.00470.00310.05630.00640.114639.011233.997188.1196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:20)
2X-RAY DIFFRACTION2(chain A and resid 21:102)
3X-RAY DIFFRACTION3(chain A and resid 103:151)
4X-RAY DIFFRACTION4(chain A and resid 152:231)

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