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- PDB-3pic: Glucuronoyl Esterase catalytic domain (Cip2_GE) from Hypocrea jecorina -

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Basic information

Entry
Database: PDB / ID: 3pic
TitleGlucuronoyl Esterase catalytic domain (Cip2_GE) from Hypocrea jecorina
ComponentsCip2
KeywordsHYDROLASE / Alpha/beta hydrolase fold / Glucuronoyl Esterase / Carbohydrate Esterase Family 15 (CE-15) / N-linked glycosylation / secreted
Function / homology
Function and homology information


lignin catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity / cellulose binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-O-methyl-glucuronoyl methylesterase / 4-O-methyl-glucuronoyl methylesterase
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsPokkuluri, P.R.
CitationJournal: Proteins / Year: 2011
Title: Structure of the catalytic domain of glucuronoyl esterase Cip2 from Hypocrea jecorina.
Authors: Pokkuluri, P.R. / Duke, N.E. / Wood, S.J. / Cotta, M.A. / Li, X.L. / Biely, P. / Schiffer, M.
History
DepositionNov 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cip2
B: Cip2
C: Cip2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8076
Polymers119,1433
Non-polymers6643
Water20,0511113
1
A: Cip2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9362
Polymers39,7141
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cip2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9362
Polymers39,7141
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cip2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9362
Polymers39,7141
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.260, 82.010, 185.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer

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Components

#1: Protein Cip2


Mass: 39714.355 Da / Num. of mol.: 3 / Fragment: Catalytic Domain (UNP residues 90-460) / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus) / References: UniProt: Q7Z9N1, UniProt: G0RV93*PLUS
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1113 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Quik screen C4 (1.4 M sodium/potassium phosphate, pH 6.9), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.91946 / Wavelength: 1.07189,1.07218
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 25, 2007
RadiationMonochromator: monochromatic / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.919461
21.071891
31.072181
ReflectionResolution: 1.9→50 Å / Num. all: 91361 / Num. obs: 91361 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4 / Num. unique all: 4131 / % possible all: 84

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-3000phasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→31.2 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 58390.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 8748 10 %RANDOM
Rwork0.195 ---
obs0.195 87710 90.1 %-
all-87710 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.6163 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å20 Å2
2---3.51 Å20 Å2
3---1.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8066 0 42 1113 9221
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.041.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.182.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 1340 9.8 %
Rwork0.247 12321 -
obs-12321 85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarb.top

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