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- PDB-4xdq: Crystal structure of a Glycoside hydrolase family protein (Rv0315... -

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Basic information

Entry
Database: PDB / ID: 4xdq
TitleCrystal structure of a Glycoside hydrolase family protein (Rv0315 ortholog) from Mycobacterium thermorestibile
ComponentsGlycoside hydrolase family protein
KeywordsHYDROLASE / structural genomics / National Institute for Allergy and Infectious Diseases / NIAID / tuberculosis / ortholog / calcium-binding / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
BENZOIC ACID / : / Glycoside hydrolase family protein
Similarity search - Component
Biological speciesMycobacterium thermoresistibile ATCC 19527 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a Glycoside hydrolase family protein (Rv0315 ortholog) from Mycobacterium thermorestibile
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,44310
Polymers29,8871
Non-polymers5569
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-27 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.550, 74.550, 95.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glycoside hydrolase family protein


Mass: 29887.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile ATCC 19527 (bacteria)
Gene: KEK_10413 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CI90

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Non-polymers , 7 types, 349 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MythA.18623.a.B2.PS02026 at 20.8 mg/mL against JCSG+ screen condition G5, 5 mM CoCl2, 5 mM CdCl2, 5 mM MgCl2, 5 mM NiCl2, 0.1 M Hepes pH 7.5, 15% PEG 3350 supplemented with 20 % EG as cryo

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 59755 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 18.076 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.061 / Χ2: 0.98 / Net I/σ(I): 28.25 / Num. measured all: 860877
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.35-1.3914.30.9580.5325.462454436543660.552100
1.39-1.420.9710.446.5260758423042300.456100
1.42-1.460.980.3627.8759553414341430.375100
1.46-1.510.9860.2959.6357571398739870.305100
1.51-1.560.990.23911.7756233389338930.248100
1.56-1.610.9940.18814.6954691376937690.195100
1.61-1.670.9950.15917.2652834364236420.164100
1.67-1.740.9960.13220.6550829349834980.137100
1.74-1.820.9980.10225.4749366339133910.106100
1.82-1.910.9990.08131.2947076322732270.083100
1.91-2.010.9990.06736.9145105309030900.069100
2.01-2.130.9990.05842.1742692293129310.06100
2.13-2.280.9990.05246.6240031274927490.054100
2.28-2.460.9990.04850.4637407257425740.05100
2.46-2.70.9990.04454.6134468238323830.046100
2.7-3.020.9990.04159.0631290217621760.042100
3.02-3.490.9990.03566.3827563192919290.036100
3.49-4.270.9990.03370.1823436165916590.034100
4.27-6.040.9990.03369.5718044132413240.034100
6.04-500.9990.03464.5594768037940.03698.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMACrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rq0

3rq0


Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.1484 / WRfactor Rwork: 0.1254 / FOM work R set: 0.9184 / SU B: 1.072 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0423 / SU Rfree: 0.0408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1479 2968 5 %RANDOM
Rwork0.1253 56708 --
obs0.1264 56708 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.65 Å2 / Biso mean: 14.451 Å2 / Biso min: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å20 Å2
2---0.56 Å20 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 26 340 2261
Biso mean--19.68 28.68 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022025
X-RAY DIFFRACTIONr_bond_other_d0.0010.021804
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9252775
X-RAY DIFFRACTIONr_angle_other_deg0.73934151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2725248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35523.26598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.76515279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3911513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02512
X-RAY DIFFRACTIONr_mcbond_it0.9611.165962
X-RAY DIFFRACTIONr_mcbond_other0.9679.733961
X-RAY DIFFRACTIONr_mcangle_it1.2271.7611205
X-RAY DIFFRACTIONr_rigid_bond_restr1.70332007
X-RAY DIFFRACTIONr_sphericity_bonded5.88351927
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 220 -
Rwork0.148 4131 -
all-4351 -
obs--99.89 %

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