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- PDB-4s24: 1.7 Angstrom Crystal Structure of of Putative Modulator of Drug A... -

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Basic information

Entry
Database: PDB / ID: 4s24
Title1.7 Angstrom Crystal Structure of of Putative Modulator of Drug Activity (apo- form) from Yersinia pestis CO92
ComponentsModulator of drug activity B
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / FLAVODOXIN-LIKE FOLD / NADPH DEHYDROGENASE (QUINONE) ACTIVITY / FLAVIN ADENINE DINUCLEOTIDE BINDING
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) / nucleotide binding
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / NADPH:quinone oxidoreductase MdaB / NADPH:quinone oxidoreductase MdaB
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.7 Angstrom Crystal Structure of of Putative Modulator of Drug Activity (apo- form) from Yersinia pestis CO92.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Modulator of drug activity B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3066
Polymers22,6091
Non-polymers6975
Water3,153175
1
A: Modulator of drug activity B
hetero molecules

A: Modulator of drug activity B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,61212
Polymers45,2192
Non-polymers1,39410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6900 Å2
ΔGint-49 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.046, 72.046, 166.766
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

21A-354-

HOH

31A-365-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Modulator of drug activity B


Mass: 22609.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: mdaB / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q7CGH8, UniProt: A0A2U2H1J1*PLUS

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Non-polymers , 5 types, 180 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 55.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Protein: 10.2 mg/ml, 0.1M Tris HCl (pH 8.3), Screen: JSCG+ (C6), 0.1M Phosphate-citrate (pH 4.2), 40% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2014 / Details: beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 29069 / Num. obs: 29069 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 15.2 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 62.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 6.2 / Num. unique all: 1417 / Rsym value: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
SHELXSphasing
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.41 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.776 / SU ML: 0.045
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16591 1407 4.9 %RANDOM
Rwork0.14852 ---
obs0.14937 27589 99.92 %-
all-27589 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.41 Å20 Å2
2--0.81 Å20 Å2
3----2.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 45 175 1751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191762
X-RAY DIFFRACTIONr_bond_other_d0.0010.021643
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9652387
X-RAY DIFFRACTIONr_angle_other_deg0.81233793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9415216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0624.45883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.68315261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.773157
X-RAY DIFFRACTIONr_chiral_restr0.1020.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0212018
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02421
X-RAY DIFFRACTIONr_mcbond_it1.7952.23840
X-RAY DIFFRACTIONr_mcbond_other1.7782.229839
X-RAY DIFFRACTIONr_mcangle_it2.7843.3291064
X-RAY DIFFRACTIONr_mcangle_other2.7843.3291065
X-RAY DIFFRACTIONr_scbond_it2.6412.551922
X-RAY DIFFRACTIONr_scbond_other2.6042.552922
X-RAY DIFFRACTIONr_scangle_other3.9923.6731324
X-RAY DIFFRACTIONr_long_range_B_refined7.21219.6232082
X-RAY DIFFRACTIONr_long_range_B_other6.9818.6962011
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 116 -
Rwork0.174 1980 -
obs-1980 100 %
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)
16.0956-5.22731.59374.9674-1.71052.3336-0.1020.14670.0797-0.08150.0010.0271-0.01440.04660.1010.0693-0.0491-0.05130.05140.01840.064947.115842.70611.4745
27.9575-2.79923.65581.3703-1.11491.7580.47140.1141-0.4843-0.0205-0.27690.28760.3031-0.059-0.19460.50060.0410.07090.36660.0260.225461.205826.3946-3.0125
31.314-0.86080.57311.2632-0.16761.8334-0.03990.21780.134-0.2204-0.01480.0266-0.01050.13560.05470.0959-0.0463-0.05650.06740.0280.062247.431643.0564-3.8813
40.8048-0.22530.31.3588-0.39090.7091-0.0944-0.12360.04640.0030.09490.1739-0.0742-0.1008-0.00050.02440.0133-0.01590.0327-0.00410.038445.193839.677913.3103
52.2986-1.2956-0.44434.57071.68621.3650.02760.1049-0.3245-0.24690.03840.36410.0205-0.1807-0.06590.0742-0.0439-0.05490.06820.0350.121540.593721.30656.3395
60.8747-0.29030.3070.29210.02682.30180.05610.0671-0.1151-0.10940.01530.16430.2318-0.0507-0.07140.1113-0.0205-0.07950.04570.00370.112340.600632.9032-2.4008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 12
2X-RAY DIFFRACTION2A13 - 18
3X-RAY DIFFRACTION3A19 - 46
4X-RAY DIFFRACTION4A47 - 125
5X-RAY DIFFRACTION5A126 - 154
6X-RAY DIFFRACTION6A155 - 194

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