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- PDB-1gpf: CHITINASE B FROM SERRATIA MARCESCENS IN COMPLEX WITH INHIBITOR PS... -

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Basic information

Entry
Database: PDB / ID: 1gpf
TitleCHITINASE B FROM SERRATIA MARCESCENS IN COMPLEX WITH INHIBITOR PSAMMAPLIN
ComponentsCHITINASE B
KeywordsHYDROLASE / CHITIN DEGRADATION / INHIBITOR PSAMMAPLIN
Function / homology
Function and homology information


chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region
Similarity search - Function
Carbohydrate-binding module superfamily 5/12 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily ...Carbohydrate-binding module superfamily 5/12 / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Ribbon / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKomander, D. / Van Aalten, D.M.
CitationJournal: Bioorg.Med.Chem. / Year: 2002
Title: Psammaplin A, a Chitinase Inhibitor Isolated from the Fijian Marine Sponge Aplysinella Rhax
Authors: Tabudravu, J.N. / Eijsink, V.G. / Gooday, G.W. / Jaspars, M. / Komander, D. / Legg, M. / Synstad, B. / Van Aalten, D.M.
History
DepositionNov 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / reflns
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHITINASE B
B: CHITINASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3245
Polymers111,0362
Non-polymers2883
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.754, 103.588, 186.065
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 CHITINASE B


Mass: 55518.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q54276, chitinase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.5 Å3/Da / Density % sol: 49.16 %
Crystal growMethod: vapor diffusion / pH: 7
Details: 2.0M AMMONIUM SULFATE, 20% GLYCEROL, HEPES PH7.0, pH 7.00
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Details: van Aalten, D.M., (2000) Proc. Natl. Acad. Sci. U.S.A., 97, 5842.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMcitrate1reservoir
30.5 M1reservoirLi2SO4
40.25 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 254155 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.4 / % possible all: 69.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 83126 / Num. measured all: 254155
Reflection shell
*PLUS
% possible obs: 69.2 % / Num. unique obs: 6368 / Rmerge(I) obs: 0.44

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E15

1e15


Resolution: 1.85→29.71 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2795287.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 840 1 %RANDOM
Rwork0.2 ---
obs0.2 82997 89.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.2425 Å2 / ksol: 0.364016 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2--6.96 Å20 Å2
3----8.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7801 0 15 614 8430
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 100 0.9 %
Rwork0.265 11031 -
obs--73.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMAMI.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.2 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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