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- PDB-4hme: Crystal structure of cold-adapted chitinase from Moritella marina... -

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Basic information

Entry
Database: PDB / ID: 4hme
TitleCrystal structure of cold-adapted chitinase from Moritella marina with a reaction product - NAG2
ComponentsChitinase 60
KeywordsHYDROLASE / Chitinase / hydrolaze / TIM-barrel / Ig-like / Immunoglobulin like domain / ChBD / Chitin binding domain
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Carbohydrate-binding module superfamily 5/12 / Carbohydrate-binding module family 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 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. ...Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Carbohydrate-binding module superfamily 5/12 / Carbohydrate-binding module family 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 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Ribbon / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å
AuthorsMalecki, P.H. / Vorgias, C.E. / Raczynska, J.E. / Rypniewski, W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium
Authors: Malecki, P.H. / Raczynska, J.E. / Vorgias, C.E. / Rypniewski, W.
History
DepositionOct 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 10, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / software
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.version
Revision 2.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4337
Polymers58,6171
Non-polymers8166
Water5,260292
1
A: Chitinase 60
hetero molecules

A: Chitinase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,86614
Polymers117,2352
Non-polymers1,63212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
Buried area7320 Å2
ΔGint-16 kcal/mol
Surface area45330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.998, 65.998, 257.537
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN.

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Components

#1: Protein Chitinase 60 /


Mass: 58617.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio marinus (bacteria) / Gene: chi60 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: B1VBB0, chitinase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DISCREPANCIES (R452H, A470T) WERE NOT INTENTIONAL MUTATIONS, AND COULD BE THE CORRECT ...THE SEQUENCE DISCREPANCIES (R452H, A470T) WERE NOT INTENTIONAL MUTATIONS, AND COULD BE THE CORRECT SEQUENCE OF THE NATIVE GENE.

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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: 2.76 Å3/Da / Density % sol: 55.47 % / Mosaicity: 0.831 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23% PEG 4000 w/v, 0.16M ammonium sulphate, 0.1M citrate buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 19, 2011
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionRedundancy: 9.1 % / Av σ(I) over netI: 19.98 / Number: 359986 / Rmerge(I) obs: 0.114 / Χ2: 1.07 / D res high: 2.07 Å / D res low: 50 Å / Num. obs: 39600 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.465099.710.0441.0649
3.544.4699.710.0661.0069.2
3.093.5499.710.0971.0899.4
2.813.0999.810.1621.089.4
2.612.8199.610.2691.1119.4
2.452.6199.510.41.0899.4
2.332.4599.410.5281.0729.4
2.232.3399.410.7011.1069.4
2.142.2399.310.8631.0538.9
2.072.1499.110.941.0587.3
ReflectionResolution: 2.07→50 Å / Num. all: 39600 / Num. obs: 39600 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rmerge(I) obs: 0.114 / Χ2: 1.073 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.07-2.147.30.9438631.058199.1
2.14-2.238.90.86339011.053199.3
2.23-2.339.40.70139141.106199.4
2.33-2.459.40.52839411.072199.4
2.45-2.619.40.439291.089199.5
2.61-2.819.40.26939201.111199.6
2.81-3.099.40.16239791.08199.8
3.09-3.549.40.09739671.089199.7
3.54-4.469.20.06640211.006199.7
4.46-5090.04441651.064199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.26 Å
Translation2.5 Å38.26 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HMC

4hmc


Resolution: 2.07→34.32 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1941 / WRfactor Rwork: 0.1597 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8417 / SU B: 9.013 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1705 / SU Rfree: 0.1519 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.152 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 1015 2.6 %RANDOM
Rwork0.1742 ---
all0.1752 39524 --
obs0.1752 39524 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.77 Å2 / Biso mean: 40.44 Å2 / Biso min: 14.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.07→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4137 0 54 292 4483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.024299
X-RAY DIFFRACTIONr_bond_other_d0.0010.022725
X-RAY DIFFRACTIONr_angle_refined_deg1.851.925875
X-RAY DIFFRACTIONr_angle_other_deg1.0463.0016666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00825.654214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07315647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4581513
X-RAY DIFFRACTIONr_chiral_restr0.120.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02851
LS refinement shellResolution: 2.069→2.123 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 51 -
Rwork0.274 2626 -
all-2677 -
obs--96.85 %
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)
10.913-0.232900.5548-0.15181.1577-0.0394-0.0737-0.0330.09130.02350.0677-0.0655-0.05820.0160.0764-0.03590.03370.0386-0.02010.09461.408924.271123.055
20.65680.2144-1.20810.1425-0.15883.6831-0.20540.0668-0.154-0.10450.0847-0.12060.1227-0.02750.12070.2316-0.06750.06010.1005-0.02920.1923-19.0961-1.472659.2488
34.1976-1.70084.71233.08430.3979.7359-0.2225-0.02720.40980.0442-0.17460.0823-0.5741-0.02040.39710.12310.016-0.00070.10180.00220.1634-26.954721.7046114.1248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 349
2X-RAY DIFFRACTION2A350 - 501
3X-RAY DIFFRACTION3A502 - 550

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