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- PDB-5x6a: Crystal structure of an endoglucanase PMO-5 -

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Basic information

Entry
Database: PDB / ID: 5x6a
TitleCrystal structure of an endoglucanase PMO-5
ComponentsEndoglucanase, putative
KeywordsHYDROLASE / endoglucanase
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / extracellular region
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 1 - #70 / Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61) / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
AA9 family lytic polysaccharide monooxygenase B
Similarity search - Component
Biological speciesNeosartorya fumigata Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShen, Q.
CitationJournal: To Be Published
Title: Crystal structure of an endoglucanase PMO-5
Authors: Shen, Q.
History
DepositionFeb 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase, putative
B: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3924
Polymers48,3432
Non-polymers492
Water9,620534
1
A: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1962
Polymers24,1721
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area9760 Å2
MethodPISA
2
B: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1962
Polymers24,1721
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.054, 48.926, 54.192
Angle α, β, γ (deg.)75.55, 88.29, 76.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Endoglucanase, putative


Mass: 24171.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata Af293 (mold) / Strain: Af293 / Gene: AFUA_4G07850 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WP32, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Magnesium chloride hexahydrate, 25% w/v Polyethylene glycol 3350, 0.1M BIS-TRIS pH 6.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→27.5 Å / Num. obs: 46666 / % possible obs: 95.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.062 / Rsym value: 0.099 / Net I/σ(I): 37.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 16.5 / Num. unique obs: 2194 / Rpim(I) all: 0.242 / Rsym value: 0.409 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data processing
AutoSolmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zud

3zud


Resolution: 1.7→27.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.5 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16585 2062 4.6 %RANDOM
Rwork0.13464 ---
obs0.13607 42644 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2---0.01 Å2-0.01 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3410 0 2 534 3946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193512
X-RAY DIFFRACTIONr_bond_other_d0.0060.023148
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9374814
X-RAY DIFFRACTIONr_angle_other_deg0.923.0027256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82825.405148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26615474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.291154
X-RAY DIFFRACTIONr_chiral_restr0.1190.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02806
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7550.9711830
X-RAY DIFFRACTIONr_mcbond_other1.7550.9681829
X-RAY DIFFRACTIONr_mcangle_it2.6381.4462284
X-RAY DIFFRACTIONr_mcangle_other2.6371.4492285
X-RAY DIFFRACTIONr_scbond_it2.941.1791682
X-RAY DIFFRACTIONr_scbond_other2.9391.1811683
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4321.6662531
X-RAY DIFFRACTIONr_long_range_B_refined6.3579.8664391
X-RAY DIFFRACTIONr_long_range_B_other6.0388.8444103
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 155 -
Rwork0.145 3070 -
obs--93.48 %

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