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- PDB-3rjx: Crystal Structure of Hyperthermophilic Endo-Beta-1,4-glucanase -

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Basic information

Entry
Database: PDB / ID: 3rjx
TitleCrystal Structure of Hyperthermophilic Endo-Beta-1,4-glucanase
ComponentsEndoglucanase FnCel5A
KeywordsHYDROLASE / thermophilic enzymes / endo-beta-1 / 4-glucanase / thermostability
Function / homology
Function and homology information


glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
: / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase, family 5 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glycoside hydrolase family 5 / Endoglucanase FnCel5A
Similarity search - Component
Biological speciesFervidobacterium nodosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsZheng, B.S. / Yang, W. / Zhao, X.Y. / Wang, Y.G. / Lou, Z.Y. / Rao, Z.H. / Feng, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of hyperthermophilic endo-beta-1,4-glucanase: implications for catalytic mechanism and thermostability.
Authors: Zheng, B. / Yang, W. / Zhao, X. / Wang, Y. / Lou, Z. / Rao, Z. / Feng, Y.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Mar 20, 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

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Assembly

Deposited unit
A: Endoglucanase FnCel5A


Theoretical massNumber of molelcules
Total (without water)37,6161
Polymers37,6161
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.712, 85.210, 53.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Endoglucanase FnCel5A / Endo-Beta-1 / 4-glucanase


Mass: 37615.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium nodosum (bacteria) / Strain: Rt17-B1 / Production host: Escherichia coli (E. coli)
References: UniProt: D4PEB3, UniProt: A7HNC0*PLUS, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.2M NaH2PO4/KH2PO4 (1:1), 0.1M sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONBSRF 1W2B21
SYNCHROTRONSSRF BL17U31
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 11, 2009
MARMOSAIC 225 mm CCD2CCDOct 23, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 12870 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→45.31 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.872 / SU B: 7.804 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.83 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25852 645 5 %RANDOM
Rwork0.17203 ---
obs0.17639 12207 84.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.277 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 0 232 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222702
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9273671
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4145312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86223.971136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3371512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212094
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6861.51564
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31122544
X-RAY DIFFRACTIONr_scbond_it2.40131138
X-RAY DIFFRACTIONr_scangle_it3.8744.51127
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 40 -
Rwork0.202 911 -
obs--87.57 %

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