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- PDB-4qp0: Crystal Structure Analysis of the Endo-1,4-beta-mannanase from Rh... -

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Basic information

Entry
Database: PDB / ID: 4qp0
TitleCrystal Structure Analysis of the Endo-1,4-beta-mannanase from Rhizomucor miehei
ComponentsEndo-beta-mannanase
KeywordsHYDROLASE / Tim Barrel / extracellular
Function / homology
Function and homology information


mannan catabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / extracellular region
Similarity search - Function
Mannan endo-1,4-beta-mannosidase-like / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
mannan endo-1,4-beta-mannosidase
Similarity search - Component
Biological speciesRhizomucor miehei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZheng, Q.J. / Peng, Z. / Liu, Y. / Yan, Q.J. / Chen, Z.Z. / Qin, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural insights into the substrate specificity and transglycosylation activity of a fungal glycoside hydrolase family 5 beta-mannosidase.
Authors: Zhou, P. / Liu, Y. / Yan, Q. / Chen, Z. / Qin, Z. / Jiang, Z.
History
DepositionJun 22, 2014Deposition site: RCSB / Processing site: PDBJ
SupersessionNov 5, 2014ID: 4L3M
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1402
Polymers40,0441
Non-polymers961
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.380, 89.719, 111.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Endo-beta-mannanase


Mass: 40043.797 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 20-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei (fungus) / Gene: Man5A / Production host: Escherichia coli (E. coli)
References: UniProt: L7SVX1, mannan endo-1,4-beta-mannosidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 80mM NaAc pH 4.6, 1.6M ammonia sulfate, 6% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 11, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. all: 20630 / Num. obs: 18610 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 31.07 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.315 / % possible all: 74

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QNO

1qno


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.053 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27364 903 5.1 %RANDOM
Rwork0.22607 ---
obs0.22861 16882 90.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2---5.49 Å20 Å2
3---6.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 5 138 2929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022866
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.9163900
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7215356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03425.319141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33115433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.333156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212236
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 56 -
Rwork0.314 1209 -
obs--96.49 %

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