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- PDB-4xxp: Crystal Structure of an Uncharacterized Protein (Rv0315 ortholog)... -

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Basic information

Entry
Database: PDB / ID: 4xxp
TitleCrystal Structure of an Uncharacterized Protein (Rv0315 ortholog) from Mycobacterium paratuberculosis
ComponentsPutative uncharacterized protein (Rv0315 ortholog)
KeywordsHYDROLASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
GH16 domain-containing protein
Similarity search - Component
Biological speciesMycobacterium paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of an Uncharacterized Protein (Rv0315 ortholog) from Mycobacterium paratuberculosis
Authors: SSGCID / Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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
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: Putative uncharacterized protein (Rv0315 ortholog)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1082
Polymers28,0841
Non-polymers241
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.030, 49.530, 55.310
Angle α, β, γ (deg.)90.000, 95.210, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a monomer, same as the asymmetric unit

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Components

#1: Protein Putative uncharacterized protein (Rv0315 ortholog)


Mass: 28083.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10) (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: MAP_1661c / Plasmid: MypaA.18623.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q73ZE2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 1.75 Å3/Da / Density % sol: 29.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: JCSG+(c1): 20% PEG-8000, 100mM Sodium phosphate dibasic/ citric acid, pH=4.2, 200mM Sodium Chloride mixed with MypaA.18623.a.B2.PS01983 at 26.32 mg/ml, tray 252788c1258195b4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 31, 2014
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 24420 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 10.02 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.046 / Χ2: 0.993 / Net I/σ(I): 35.5 / Num. measured all: 293026
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.647.40.9740.218.0411808190015860.22583.5
1.64-1.690.9850.18110.3114179183615700.19185.5
1.69-1.740.9870.16211.4614183178415570.17187.3
1.74-1.790.9930.13113.9614583175415760.13889.9
1.79-1.850.9950.11515.7714634169415540.12291.7
1.85-1.910.9970.09719.1815055166415670.10294.2
1.91-1.980.9980.07823.5714703155814980.08296.1
1.98-2.070.9980.06628.3214852152214940.06998.2
2.07-2.160.9980.06131.9414712144814370.06499.2
2.16-2.260.9990.05735.7414852140514040.0699.9
2.26-2.390.9990.05439.6116249132513210.05799.7
2.39-2.530.9990.05144.5616626125912580.05399.9
2.53-2.70.9990.04748.4116346117311730.049100
2.7-2.920.9990.04453.0216524112711230.04699.6
2.92-3.20.9990.03962.97162869989980.041100
3.2-3.5810.03680.52182209349340.037100
3.58-4.1310.03387.2171408248240.034100
4.13-5.0610.02989.47146267017000.0399.9
5.06-7.1610.03585.44114925435430.035100
7.1610.03786.1659563063030.03899

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PQ9

4pq9


Resolution: 1.6→36.83 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1706 2068 8.47 %
Rwork0.1401 22352 -
obs0.1427 24420 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.88 Å2 / Biso mean: 13.5548 Å2 / Biso min: 4.02 Å2
Refinement stepCycle: final / Resolution: 1.6→36.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 1 259 1895
Biso mean--6.85 26.03 -
Num. residues----207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081704
X-RAY DIFFRACTIONf_angle_d1.1572337
X-RAY DIFFRACTIONf_chiral_restr0.057224
X-RAY DIFFRACTIONf_plane_restr0.006305
X-RAY DIFFRACTIONf_dihedral_angle_d12.408570
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63710.20531090.16061325143483
1.6371-1.67810.18431360.14541297143385
1.6781-1.72350.18741290.14171377150687
1.7235-1.77420.18331250.13871373149889
1.7742-1.83140.17271260.14021435156191
1.8314-1.89690.17681280.14031488161694
1.8969-1.97280.18141450.14041482162795
1.9728-2.06260.18461320.14151544167698
2.0626-2.17140.1761570.14141542169999
2.1714-2.30740.16951630.14315461709100
2.3074-2.48550.17911440.151415751719100
2.4855-2.73550.18361350.158915791714100
2.7355-3.13120.19741650.152415481713100
3.1312-3.94430.14271370.123916061743100
3.9443-36.83960.1321370.125316351772100
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)
10.7197-0.10740.02611.42650.37411.2446-0.03120.1564-0.088-0.15680.0205-0.04420.00340.05350.04270.0614-0.01430.00940.0851-0.020.0769-4.0374-15.127461.6231
21.3558-0.6543-0.00451.1830.41381.2139-0.03360.01320.09080.06280.0576-0.1879-0.10680.15230.0180.0539-0.01270.00040.07150.00890.07867.445-8.463273.0936
30.75290.12130.01660.92710.3060.6069-0.0247-0.0239-0.03280.07780.01970.0453-0.02040.02740.00360.05830.00040.00410.05820.00470.0463-0.7668-7.702874.1616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 140 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 190 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 275 )A0

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