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- PDB-6mzz: Fluoroacetate dehalogenase, room temperature structure, using fir... -

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Basic information

Entry
Database: PDB / ID: 6mzz
TitleFluoroacetate dehalogenase, room temperature structure, using first 1 degree of total 3 degree oscillation
ComponentsFluoroacetate dehalogenaseHaloacetate dehalogenase
KeywordsHYDROLASE / Dehalogenase / defluorinase
Function / homology
Function and homology information


haloacetate dehalogenase / haloacetate dehalogenase activity / epoxide hydrolase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fluoroacetate dehalogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFinke, A.D. / Wierman, J.L. / Pare-Labrosse, O. / Sarrachini, A. / Besaw, J. / Mehrabi, P. / Gruner, S.M. / Miller, R.J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
CitationJournal: IUCrJ / Year: 2019
Title: Fixed-target serial oscillation crystallography at room temperature.
Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / ...Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / Szebenyi, D.M.E. / Gruner, S.M. / Miller, R.J.D. / Finke, A.D.
History
DepositionNov 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluoroacetate dehalogenase
B: Fluoroacetate dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1873
Polymers68,1472
Non-polymers401
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-22 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.600, 79.100, 83.800
Angle α, β, γ (deg.)90.000, 103.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Fluoroacetate dehalogenase / Haloacetate dehalogenase


Mass: 34073.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1163 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NAM1, haloacetate dehalogenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 16-20% PEG 3350, 100mM Tris-Cl pH 8.5, and 200mM CaCl2.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: G3 / Wavelength: 1.216 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 1, 2018
RadiationMonochromator: W/B4C mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.216 Å / Relative weight: 1
ReflectionResolution: 1.8→39.55 Å / Num. obs: 48562 / % possible obs: 99.02 % / Redundancy: 5.7 % / Biso Wilson estimate: 34.41 Å2 / CC1/2: 0.954 / Rpim(I) all: 0.1648 / Rrim(I) all: 0.4132 / Net I/σ(I): 4.71
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 4680 / CC1/2: 0.0739 / Rpim(I) all: 3.646 / Rrim(I) all: 8.37
Serial crystallography measurementCollimation: Compound refractive lens
Serial crystallography sample deliveryDescription: Si fixed target / Method: fixed target
Serial crystallography data reductionCrystal hits: 1082 / Frames indexed: 1970 / Frames total: 32000

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FSX

6fsx


Resolution: 1.8→39.55 Å / SU ML: 0.3456 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0932
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 2442 5.03 %Rnadom
Rwork0.1749 ---
obs0.1766 48558 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 1 217 4922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754914
X-RAY DIFFRACTIONf_angle_d0.95266698
X-RAY DIFFRACTIONf_chiral_restr0.0504684
X-RAY DIFFRACTIONf_plane_restr0.0063879
X-RAY DIFFRACTIONf_dihedral_angle_d16.07843964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.49681360.50152563X-RAY DIFFRACTION94.87
1.84-1.880.40211480.40672663X-RAY DIFFRACTION98.46
1.88-1.920.44241420.37022709X-RAY DIFFRACTION98.51
1.92-1.970.33921430.31062713X-RAY DIFFRACTION98.99
1.97-2.020.29741430.28252666X-RAY DIFFRACTION98.8
2.02-2.080.3211450.26372765X-RAY DIFFRACTION99.28
2.08-2.150.26411420.24862650X-RAY DIFFRACTION98.94
2.15-2.230.26691430.22722716X-RAY DIFFRACTION99.41
2.23-2.310.25951460.20392752X-RAY DIFFRACTION99.59
2.31-2.420.23891420.182719X-RAY DIFFRACTION99.31
2.42-2.550.20481440.17532696X-RAY DIFFRACTION99.4
2.55-2.710.22991440.17362725X-RAY DIFFRACTION99.69
2.71-2.920.19281440.16942730X-RAY DIFFRACTION99.65
2.92-3.210.22511440.16292775X-RAY DIFFRACTION99.86
3.21-3.670.17221430.14052718X-RAY DIFFRACTION99.86
3.67-4.630.15051460.11862787X-RAY DIFFRACTION99.76
4.63-40.840.16291470.14942769X-RAY DIFFRACTION98.95

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