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- PDB-4xzb: endo-glucanase GsCelA P1 -

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Basic information

Entry
Database: PDB / ID: 4xzb
Titleendo-glucanase GsCelA P1
ComponentsCelA
KeywordsHYDROLASE / endo-glucanase
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus sp. 70PC53 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLee, C.C. / Chang, C.J. / Ho, T.H.D. / Chao, Y.C. / Wang, A.H.J.
CitationJournal: To Be Published
Title: Structure of endo-glucanase GsCelA P1 at 1.62 Angstroms
Authors: Lee, C.C. / Chang, C.J. / Ho, T.H.D. / Chao, Y.C. / Wang, A.H.J.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CelA


Theoretical massNumber of molelcules
Total (without water)35,8021
Polymers35,8021
Non-polymers00
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12440 Å2
Unit cell
Length a, b, c (Å)40.957, 71.673, 92.248
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 CelA


Mass: 35801.734 Da / Num. of mol.: 1 / Fragment: UNP residues 25-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus sp. 70PC53 (bacteria) / Gene: celA / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: C5H6X3, 3-hydroxyisobutyryl-CoA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6 / Details: 16%(w/v) PEG4000, 0.2M imidazole malate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→30 Å / Num. obs: 35214 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 32.4
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Cootdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZT

3pzt


Resolution: 1.62→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.355 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17824 1760 5.1 %RANDOM
Rwork0.15931 ---
obs0.1603 33088 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.905 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0 Å2
2---0.07 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.62→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 0 398 2911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192584
X-RAY DIFFRACTIONr_bond_other_d0.0010.022351
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9173517
X-RAY DIFFRACTIONr_angle_other_deg0.78735395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2545311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27724.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58715406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1381516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
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_it0.6960.9781247
X-RAY DIFFRACTIONr_mcbond_other0.6940.9751246
X-RAY DIFFRACTIONr_mcangle_it1.2011.4611557
X-RAY DIFFRACTIONr_mcangle_other1.2011.4641558
X-RAY DIFFRACTIONr_scbond_it1.1361.1621337
X-RAY DIFFRACTIONr_scbond_other1.1361.1651338
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8411.691961
X-RAY DIFFRACTIONr_long_range_B_refined5.10610.0193463
X-RAY DIFFRACTIONr_long_range_B_other4.5838.913213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.621→1.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 109 -
Rwork0.243 2085 -
obs--86.72 %

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