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- PDB-2nly: Crystal structure of protein BH1492 from Bacillus halodurans, Pfa... -

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Basic information

Entry
Database: PDB / ID: 2nly
TitleCrystal structure of protein BH1492 from Bacillus halodurans, Pfam DUF610
ComponentsDivergent polysaccharide deacetylase hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / divergent polysaccharide deacetylase / pfam04748 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


carbohydrate metabolic process / metal ion binding
Similarity search - Function
Divergent polysaccharide deacetylase / Divergent polysaccharide deacetylase / Glycoside hydrolase/deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJin, X. / Sauder, J.M. / Wasserman, S. / Smith, D. / Burley, S.K. / Shapiro, L. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein BH1492 from Bacillus halodurans C-125
Authors: Jin, X. / Sauder, J.M. / Wasserman, S. / Smith, D. / Burley, S.K. / Shapiro, L.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Divergent polysaccharide deacetylase hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0642
Polymers26,9991
Non-polymers651
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.153, 113.517, 63.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is the monomer in the asymmetric unit.

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Components

#1: Protein Divergent polysaccharide deacetylase hypothetical protein / BH1492 protein


Mass: 26998.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH1492 / Plasmid: pSGX4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+RIL / References: UniProt: Q9KCS7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 22% PEG 8K, 100mM Sodium Acetate (pH 4.5), 200mM Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.5→45.8 Å / Num. all: 10618 / Num. obs: 10606 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.079 / Rsym value: 0.06 / Net I/σ(I): 24.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1039 / Rsym value: 0.393 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.89 / SU B: 18.872 / SU ML: 0.214 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.409 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27314 502 4.8 %RANDOM
Rwork0.22195 ---
all0.225 10606 --
obs0.22451 9949 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.523 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 1 33 1684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221677
X-RAY DIFFRACTIONr_angle_refined_deg2.0691.9772264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6325214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4242568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.97315308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.866159
X-RAY DIFFRACTIONr_chiral_restr0.1850.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021230
X-RAY DIFFRACTIONr_nbd_refined0.2430.2792
X-RAY DIFFRACTIONr_nbtor_refined0.320.21133
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0190.21
X-RAY DIFFRACTIONr_mcbond_it0.7961.51104
X-RAY DIFFRACTIONr_mcangle_it1.3521743
X-RAY DIFFRACTIONr_scbond_it1.9273624
X-RAY DIFFRACTIONr_scangle_it3.0884.5521
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 40 -
Rwork0.245 709 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.93 Å / Origin y: 39.451 Å / Origin z: 35.509 Å
111213212223313233
T-0.0271 Å20.0692 Å20.0555 Å2--0.0464 Å20.0013 Å2--0.0192 Å2
L1.9305 °2-0.7462 °20.3086 °2-3.7244 °21.6858 °2--4.7606 °2
S0.079 Å °0.2231 Å °-0.1522 Å °-0.1711 Å °0.0694 Å °-0.5084 Å °0.2982 Å °0.6183 Å °-0.1484 Å °

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