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- PDB-5hcw: Crystal structure of C-As lyase with mutations Y100H and V102F (m... -

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Basic information

Entry
Database: PDB / ID: 5hcw
TitleCrystal structure of C-As lyase with mutations Y100H and V102F (monoclinic form)
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsLYASE / cupin fold
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Glyoxalase/bleomycin resistance protein/dioxygenase
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.785 Å
AuthorsVenkadesh, S. / Yoshinaga, M. / Kandavelu, P. / Sankaran, B. / Rosen, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 GM55425 United States
CitationJournal: To Be Published
Title: Crystal structure of C-As lyase with mutations Y100H and V102F (monoclinic form)
Authors: Venkadesh, S. / Yoshinaga, M. / Kandavelu, P. / Sankaran, B. / Rosen, B.P.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
C: Glyoxalase/bleomycin resistance protein/dioxygenase
D: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)53,9044
Polymers53,9044
Non-polymers00
Water91951
1
A: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)13,4761
Polymers13,4761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)13,4761
Polymers13,4761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)13,4761
Polymers13,4761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)13,4761
Polymers13,4761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)26,9522
Polymers26,9522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-27 kcal/mol
Surface area10380 Å2
MethodPISA
6
C: Glyoxalase/bleomycin resistance protein/dioxygenase
D: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)26,9522
Polymers26,9522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-28 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.925, 79.683, 70.862
Angle α, β, γ (deg.)90.00, 101.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glyoxalase/bleomycin resistance protein/dioxygenase / C-P lyase


Mass: 13476.099 Da / Num. of mol.: 4 / Fragment: UNP residues 1-123 / Mutation: Y100H, V102F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081) (bacteria)
Strain: ATCC 19995 / DSM 43183 / JCM 3096 / NCIMB 10081 / Gene: Tcur_4156 / Production host: Escherichia coli (E. coli) / References: UniProt: D1A230
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.21 Å3/Da / Density % sol: 44.25 % / Description: Plate like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% Peg 4000, 0.1 M Na acetate, 0.2 M NH4 sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 11, 2015
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 11380 / % possible obs: 96 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.9
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2 / % possible all: 77.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.785→35.429 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2825 492 4.8 %
Rwork0.1943 --
obs0.1985 10244 86.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.785→35.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 0 51 3313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013338
X-RAY DIFFRACTIONf_angle_d1.4174569
X-RAY DIFFRACTIONf_dihedral_angle_d15.0121125
X-RAY DIFFRACTIONf_chiral_restr0.09530
X-RAY DIFFRACTIONf_plane_restr0.006603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7847-3.06480.3581740.2241514X-RAY DIFFRACTION54
3.0648-3.50790.32271420.21732626X-RAY DIFFRACTION95
3.5079-4.41830.30351330.18612820X-RAY DIFFRACTION100
4.4183-35.43150.2341430.18392792X-RAY DIFFRACTION98

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