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- PDB-3dd5: Glomerella cingulata E600-cutinase complex -

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Basic information

Entry
Database: PDB / ID: 3dd5
TitleGlomerella cingulata E600-cutinase complex
ComponentsCutinase
KeywordsHYDROLASE / catalytic triad / Secreted / Serine esterase
Function / homology
Function and homology information


cutinase / cutinase activity / carbohydrate catabolic process / extracellular region
Similarity search - Function
Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIETHYL PHOSPHONATE / Cutinase 1
Similarity search - Component
Biological speciesGlomerella cingulata (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNyon, M.P. / Rice, D.W. / Berrisford, J.M. / Hounslow, A.M. / Moir, A.J.G. / Huang, H. / Nathan, S. / Mahadi, N.M. / Farah Diba, A.B. / Craven, C.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Catalysis by Glomerella cingulata Cutinase Requires Conformational Cycling between the Active and Inactive States of Its Catalytic Triad
Authors: Nyon, M.P. / Rice, D.W. / Berrisford, J.M. / Hounslow, A.M. / Moir, A.J.G. / Huang, H. / Nathan, S. / Mahadi, N.M. / Bakar, F.D.A. / Craven, C.J.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cutinase
B: Cutinase
C: Cutinase
D: Cutinase
E: Cutinase
F: Cutinase
G: Cutinase
H: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,86316
Polymers168,7588
Non-polymers1,1058
Water724
1
A: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0951
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0951
Non-polymers1381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0951
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0951
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0951
Non-polymers1381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0951
Non-polymers1381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0951
Non-polymers1381
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2332
Polymers21,0951
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
B: Cutinase
hetero molecules

C: Cutinase
hetero molecules

A: Cutinase
F: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9328
Polymers84,3794
Non-polymers5524
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation2_546-x,y-1/2,-z+11
crystal symmetry operation2_646-x+1,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-50 kcal/mol
Surface area28960 Å2
MethodPISA
10
D: Cutinase
hetero molecules

G: Cutinase
hetero molecules

E: Cutinase
hetero molecules

H: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9328
Polymers84,3794
Non-polymers5524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area4590 Å2
ΔGint-48 kcal/mol
Surface area28970 Å2
MethodPISA
11
A: Cutinase
hetero molecules

B: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4664
Polymers42,1902
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area1310 Å2
ΔGint-12 kcal/mol
Surface area15520 Å2
MethodPISA
12
C: Cutinase
hetero molecules

F: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4664
Polymers42,1902
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area1360 Å2
ΔGint-14 kcal/mol
Surface area15390 Å2
MethodPISA
13
D: Cutinase
hetero molecules

E: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4664
Polymers42,1902
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area1360 Å2
ΔGint-11 kcal/mol
Surface area15590 Å2
MethodPISA
14
G: Cutinase
hetero molecules

H: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4664
Polymers42,1902
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area1320 Å2
ΔGint-13 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.47, 117.37, 95.24
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cutinase / Cutin hydrolase


Mass: 21094.807 Da / Num. of mol.: 8 / Fragment: residues 31-224
Source method: isolated from a genetically manipulated source
Details: Cutinase (GenBank accession no. AF444194) (amino acids 31-224)
Source: (gene. exp.) Glomerella cingulata (fungus) / Plasmid details: modified pET32b / Plasmid: pET32b_CutA / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: P11373, cutinase
#2: Chemical
ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H11O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, CUTI_COLGL.

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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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.1M magnesium acetate, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2006 / Details: Osmic Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 47279 / Num. obs: 47279 / % possible obs: 98 % / Redundancy: 2.9 % / Biso Wilson estimate: 40.345 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6694 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DCN

3dcn


Resolution: 2.6→19.8 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.828 / SU B: 13.04 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.603 / ESU R Free: 0.376
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2391 5.1 %RANDOM
Rwork0.215 ---
obs0.219 44886 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.304 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.02 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11428 0 64 4 11496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.96315936
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93151539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.18324.074459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.376151764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.691564
X-RAY DIFFRACTIONr_chiral_restr0.1070.21831
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028884
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.25458
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.28088
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2389
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.2112
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 196 -
Rwork0.31 3108 -
obs--94.67 %

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