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- PDB-9ngb: truncated cis-CaaD -

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Basic information

Entry
Database: PDB / ID: 9ngb
Titletruncated cis-CaaD
ComponentsCis-3-chloroacrylic acid dehalogenase
KeywordsHYDROLASE / Tautomerase / cis-CaaD
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / Cis-3-chloroacrylic acid dehalogenase
Function and homology information
Biological speciescoryneform bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSilva, K. / Geiger, J.H. / Draths, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: truncated cis-CaaD
Authors: Silva, K. / Geiger, J.H. / Draths, K.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2272
Polymers15,1311
Non-polymers961
Water48627
1
A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules

A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules

A: Cis-3-chloroacrylic acid dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6816
Polymers45,3933
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8110 Å2
ΔGint-98 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.266, 59.266, 57.816
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

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Components

#1: Protein Cis-3-chloroacrylic acid dehalogenase


Mass: 15130.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) coryneform bacterium (bacteria) / Gene: cis-caaD / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VPE5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 3682 / % possible obs: 91.3 % / Redundancy: 13.1 % / Biso Wilson estimate: 33.72 Å2 / Rpim(I) all: 0.072 / Net I/σ(I): 13.48
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 192 / Rpim(I) all: 0.227

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.63 Å / SU ML: 0.3746 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.3761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.301 693 10.12 %
Rwork0.2093 6154 -
obs0.2185 3661 87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 5 27 963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079956
X-RAY DIFFRACTIONf_angle_d0.89131293
X-RAY DIFFRACTIONf_chiral_restr0.0562138
X-RAY DIFFRACTIONf_plane_restr0.0092170
X-RAY DIFFRACTIONf_dihedral_angle_d6.1621129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.70.28761420.23061308X-RAY DIFFRACTION92.83
2.7-2.970.30331620.20671386X-RAY DIFFRACTION99.81
2.97-3.40.28341490.19051385X-RAY DIFFRACTION97.89
3.4-4.280.29441350.20581149X-RAY DIFFRACTION82.1
4.28-29.630.32541050.2211926X-RAY DIFFRACTION65.59

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