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- PDB-3nco: Crystal structure of FnCel5A from F. nodosum Rt17-B1 -

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Basic information

Entry
Database: PDB / ID: 3nco
TitleCrystal structure of FnCel5A from F. nodosum Rt17-B1
Components
  • Endoglucanase FnCel5A
  • peptide (ALA)(ASN)(GLU)
  • peptide (ALA)(ASP)(GLN)
KeywordsHYDROLASE / FnCel5A / F. nodosum Rt17-B1
Function / homology
Function and homology information


glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region
Similarity search - Function
: / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Glycoside hydrolase family 5 / Endoglucanase FnCel5A
Similarity search - Component
Biological speciesFervidobacterium nodosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsZheng, B.S. / Yang, W. / Wang, Y. / Lou, Z.Y. / Rao, Z.H. / Feng, Y.
CitationJournal: To be Published
Title: Crystal structure of FnCel5A from F. nodosum Rt17-B1
Authors: Zheng, B.S. / Rao, Z.H.
History
DepositionJun 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase FnCel5A
B: Endoglucanase FnCel5A
D: peptide (ALA)(ASN)(GLU)
E: peptide (ALA)(ASP)(GLN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6518
Polymers76,2714
Non-polymers3804
Water15,601866
1
A: Endoglucanase FnCel5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9933
Polymers37,8031
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase FnCel5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9933
Polymers37,8031
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: peptide (ALA)(ASN)(GLU)


  • defined by author&software
  • 332 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3321
Polymers3321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: peptide (ALA)(ASP)(GLN)


  • defined by author&software
  • 332 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3321
Polymers3321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.966, 85.769, 107.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoglucanase FnCel5A


Mass: 37803.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium nodosum (bacteria) / Strain: Rt17-B1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: D4PEB3, UniProt: A7HNC0*PLUS, cellulase
#2: Protein/peptide peptide (ALA)(ASN)(GLU)


Mass: 332.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Protein/peptide peptide (ALA)(ASP)(GLN)


Mass: 332.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9798, 0.9795, 0.9600
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.97951
30.961
ReflectionResolution: 1.5→50 Å / Num. all: 122364 / Num. obs: 121477 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.67→1.75 Å / Rmerge(I) obs: 0.407 / Num. unique all: 12477 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.803 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26344 5661 5 %RANDOM
Rwork0.2213 ---
obs0.22334 106721 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.414 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2--0.3 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5269 0 20 866 6155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225455
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.937410
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2665627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10524.058276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34115905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7551524
X-RAY DIFFRACTIONr_chiral_restr0.1210.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024216
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22838
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.23741
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2594
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1481.53234
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58425119
X-RAY DIFFRACTIONr_scbond_it2.9432643
X-RAY DIFFRACTIONr_scangle_it4.3534.52291
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 375 -
Rwork0.411 6907 -
obs--82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77570.1903-0.05450.5292-0.10310.378-0.00160.08930.03070.0290.00670.0126-0.00970.0019-0.0051-0.03390.0023-0.0016-0.0287-0.0012-0.030619.797718.94481.2337
20.87420.19880.0480.47950.10510.3622-0.0010.067-0.02580.02350.0063-0.02360.0214-0.0036-0.0053-0.0270.00270.0015-0.03450.0026-0.037421.1044-18.91891.2367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 320
2X-RAY DIFFRACTION2B9 - 320

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