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- PDB-1aq6: STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS -

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Basic information

Entry
Database: PDB / ID: 1aq6
TitleSTRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS
ComponentsL-2-HALOACID DEHALOGENASE
KeywordsDEHALOGENASE / L-2-HALOACID DEHALOGENASE
Function / homology
Function and homology information


(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity
Similarity search - Function
L-2-Haloacid dehalogenase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...L-2-Haloacid dehalogenase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / 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
FORMIC ACID / (S)-2-haloacid dehalogenase
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsRidder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: Three-dimensional structure of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate.
Authors: Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Janssen, D.B. / Dijkstra, B.W.
#1: Journal: Protein Sci. / Year: 1995
Title: Crystallization and Preliminary X-Ray Analysis of L-2-Haloacid Dehalogenase from Xanthobacter Autotrophicus Gj10
Authors: Ridder, I.S. / Rozeboom, H.J. / Kingma, J. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionAug 7, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 7, 2021Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / refine / struct_site
Item: _diffrn_source.pdbx_synchrotron_site / _refine.ls_percent_reflns_obs ..._diffrn_source.pdbx_synchrotron_site / _refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-2-HALOACID DEHALOGENASE
B: L-2-HALOACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1275
Polymers54,9892
Non-polymers1383
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-29 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.246, 84.160, 91.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.996674, -0.007367, 0.08116), (0.007103, -0.999968, -0.003545), (0.081184, -0.002956, 0.996695)
Vector: 112.678, -0.129, -4.546)

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Components

#1: Protein L-2-HALOACID DEHALOGENASE


Mass: 27494.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: SUBSTRATE ANALOGUE FORMATE PRESENT IN BOTH ACTIVE SITES
Source: (natural) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / References: UniProt: Q60099, (S)-2-haloacid dehalogenase
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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 Å3/Da / Density % sol: 38 %
Crystal growMethod: macroseeding / pH: 7
Details: MACROSEEDING, DROP: 16% PEG8000, 200 MM SODIUM FORMATE, 100 MM BIS-TRIS PH 7.0; WELL: 22% PEG8000, 200 MM SODIUM FORMATE, 100 MM BIS-TRIS PH 7.0, macroseeding
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding / PH range low: 7 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
216 %(w/v)PEG80001drop
3200 mMsodium formate1drop
4100 mMBis-Tris1drop
520-22 %PEG80001reservoir
6200 mMsodium formate1reservoir
7100 mMbis-Tris1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.883
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 30, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.883 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 32507 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 13.5 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.2
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 6 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 438845

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Processing

Software
NameClassification
PHASESphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.95→5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1501 5 %RANDOM
Rwork0.19 ---
obs0.192 30835 97.9 %-
Displacement parametersBiso mean: 21.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.95→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 9 334 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0812.5
X-RAY DIFFRACTIONp_mcangle_it1.4612
X-RAY DIFFRACTIONp_scbond_it2.1673
X-RAY DIFFRACTIONp_scangle_it2.9614
X-RAY DIFFRACTIONp_plane_restr0.02010.03
X-RAY DIFFRACTIONp_chiral_restr0.0960.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2470.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1830.3
X-RAY DIFFRACTIONp_planar_tor3.67
X-RAY DIFFRACTIONp_staggered_tor17.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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