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- PDB-3uam: Crystal structure of a chitin binding domain from Burkholderia ps... -

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Basic information

Entry
Database: PDB / ID: 3uam
TitleCrystal structure of a chitin binding domain from Burkholderia pseudomallei
ComponentsChitin binding domain
KeywordsPROTEIN BINDING / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


chitin-binding protein cbp21 / : / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
NITRATE ION / Chitin binding domain
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement, molecular replacement / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a chitin binding domain from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Gardberg, A. / Armour, B. / Staker, B. / Stewart, L.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Chitin binding domain
B: Chitin binding domain
C: Chitin binding domain
D: Chitin binding domain
E: Chitin binding domain
F: Chitin binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,73714
Polymers145,1506
Non-polymers5868
Water16,916939
1
A: Chitin binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4084
Polymers24,1921
Non-polymers2163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chitin binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2542
Polymers24,1921
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chitin binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2542
Polymers24,1921
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chitin binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2842
Polymers24,1921
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Chitin binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2542
Polymers24,1921
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Chitin binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2842
Polymers24,1921
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.920, 74.780, 74.770
Angle α, β, γ (deg.)120.04, 98.04, 102.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Chitin binding domain


Mass: 24191.709 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_0114 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JY22
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 290 K / pH: 6.77
Details: Internal tracking number 225965. PACT optimization screen F5 well F8. 0.1M Bis Tris propane pH 6.77, 200mM sodium nitrate, 20.54% w/v PEG3500, 20% Ethylene Glycol Cryo. BupsA.17478.a.A1 ...Details: Internal tracking number 225965. PACT optimization screen F5 well F8. 0.1M Bis Tris propane pH 6.77, 200mM sodium nitrate, 20.54% w/v PEG3500, 20% Ethylene Glycol Cryo. BupsA.17478.a.A1 PW31202 21mg/ml, vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→45.013 Å / Num. obs: 82444 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.42 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.42
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.9 / % possible all: 93.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5 Å23.42 Å
Translation5 Å23.42 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: PDB ENTRY 2BEM

2bem


Resolution: 2→45.013 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.773 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 4105 5 %RANDOM
Rwork0.173 ---
obs0.175 82443 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.09 Å20.13 Å2
2---0.34 Å2-0.13 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→45.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9403 0 38 939 10380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.029810
X-RAY DIFFRACTIONr_bond_other_d0.0010.026595
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9313428
X-RAY DIFFRACTIONr_angle_other_deg0.852315909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40551197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81623.406505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.124151397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6511577
X-RAY DIFFRACTIONr_chiral_restr0.0790.21374
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022162
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 298 -
Rwork0.205 5489 -
obs--93.84 %
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)
10.8949-0.1461-0.10050.9172-0.31851.16260.02350.0544-0.0208-0.0439-0.00180.0064-0.04050.045-0.02170.0086-0.0035-0.00180.0228-0.01410.01320.6614-0.73461.8296
21.0514-0.09870.08171.01-0.05920.9009-0.01140.0906-0.1084-0.00520.01580-0.02880.0346-0.00440.0049-0.010.00630.0446-0.02030.018326.831-2.189327.8881
30.4666-0.0025-0.35121.34390.36781.37550.02230.01010.0681-0.04150.00830.12450.0389-0.0301-0.03060.01070.005-0.00760.02910.01380.05654.1914-35.800817.0162
40.69720.0924-0.07140.9108-0.30551.243-0.0170.00550.1034-0.0835-0.01240.0716-0.0499-0.04620.02940.02710.0046-0.01670.0138-0.01410.040339.0878-3.3243-8.6135
50.7288-0.3637-0.46261.61640.67731.30380.0108-0.0648-0.04560.2179-0.0676-0.04530.06190.0330.05690.0361-0.0185-0.00930.02270.02010.041325.798829.72526.0891
61.2513-1.066-0.25952.48670.73540.6696-0.1667-0.2639-0.03760.29140.2043-0.0880.13170.0703-0.03760.07890.03-0.0040.08210.01070.010713.898-29.6115-19.6661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 214
2X-RAY DIFFRACTION2B17 - 214
3X-RAY DIFFRACTION3C23 - 214
4X-RAY DIFFRACTION4D16 - 214
5X-RAY DIFFRACTION5E23 - 214
6X-RAY DIFFRACTION6F16 - 214

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