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- PDB-1qq5: STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS -

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Basic information

Entry
Database: PDB / ID: 1qq5
TitleSTRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS
ComponentsPROTEIN (L-2-HALOACID DEHALOGENASE)
KeywordsHYDROLASE / 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 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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 / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsRidder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase.
Authors: Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#1: 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.
#2: 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
DepositionJun 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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_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: PROTEIN (L-2-HALOACID DEHALOGENASE)
B: PROTEIN (L-2-HALOACID DEHALOGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1414
Polymers55,0492
Non-polymers922
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-35 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.050, 83.928, 91.227
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 PROTEIN (L-2-HALOACID DEHALOGENASE)


Mass: 27524.398 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


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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 growpH: 7 / Details: pH 7.00
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: used to seeding, Ridder, I.S., (1995) Protein Sci., 4, 2619.
PH range low: 7 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mg/mlprotein1drop
215 %PEG80001drop
3200 mMsodium formate1drop
4100 mMBis-Tris1drop
520 %PEG80001reservoir
6200 mMsodium formate1reservoir
7100 mMbis-Tris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9475
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9475 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 63057 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 24.7
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.351 / % possible all: 81.4
Reflection
*PLUS
Highest resolution: 1.52 Å / Lowest resolution: 30 Å / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Num. measured all: 306585 / Biso Wilson estimate: 19.4 Å2
Reflection shell
*PLUS
% possible obs: 81.4 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AQ6

1aq6


Resolution: 1.52→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 2391656.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: WEIGTH ON OMEGA DIHEDRAL ANGLE SET TO 20% OF VALUE IN CNS FORCE FIELD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3201 5.1 %EXTENSION OF 1AQ6 FREE SET
Rwork0.204 ---
obs0.204 62986 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.22 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--2.49 Å20 Å2
3----3.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.52→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 0 577 4507
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it2.622
X-RAY DIFFRACTIONc_scangle_it3.942.5
LS refinement shellResolution: 1.52→1.62 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 477 5.2 %
obs--81.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_1999.PARAMPROTEIN_1999.TOP
X-RAY DIFFRACTION2WATER_REP.PARA
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Rfactor Rfree: 0.301

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