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- PDB-7rkb: Crystal Structure of Putative Pterin Binding Protein (PruR) from ... -

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Basic information

Entry
Database: PDB / ID: 7rkb
TitleCrystal Structure of Putative Pterin Binding Protein (PruR) from Klebsiella pneumoniae in Complex with Neopterin
ComponentsPterin Binding Protein
KeywordsPTERIN BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / PruR
Function / homologySulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Alpha-Beta Complex / Alpha Beta / L-NEOPTERIN / Molybdopterin-dependent oxidoreductase
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae SA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of Putative Pterin Binding Protein (PruR) from Klebsiella pneumoniae in Complex with Neopterin.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,88311
Polymers17,0691
Non-polymers81510
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-83 kcal/mol
Surface area7490 Å2
Unit cell
Length a, b, c (Å)83.521, 83.521, 45.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Pterin Binding Protein


Mass: 17068.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae SA1 (bacteria)
Gene: RJA_09115 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: A0A3F3BDC8
#2: Chemical ChemComp-NEU / L-NEOPTERIN / 2-AMINO-6-((1S,2R)-1,2,3-TRIHYDROXYPROPYL)PTERIDIN-4(3H)-ONE


Mass: 253.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 8.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris, pH 8.3, 2 mM Neopterin against Classics II screen G5 (0.2 M lithium sulfate, 0.1 M Tris, pH 8.5, 25% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2019 / Details: Be
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 5990 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 57 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.045 / Rrim(I) all: 0.163 / Rsym value: 0.157 / Χ2: 1.261 / Net I/σ(I): 20.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.675 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 298 / CC1/2: 0.709 / CC star: 0.911 / Rpim(I) all: 0.461 / Rsym value: 1.675 / Χ2: 1.004 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.53 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 21.645 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.827 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 635 10.7 %RANDOM
Rwork0.1881 ---
obs0.1928 5324 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.73 Å2 / Biso mean: 68.845 Å2 / Biso min: 39.13 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å20 Å20 Å2
2---2.38 Å2-0 Å2
3---4.76 Å2
Refinement stepCycle: final / Resolution: 2.5→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 43 20 1215
Biso mean--83.99 56.26 -
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0121222
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161151
X-RAY DIFFRACTIONr_angle_refined_deg1.141.651659
X-RAY DIFFRACTIONr_angle_other_deg0.6651.5592685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9575147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.913105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg4.2810195
X-RAY DIFFRACTIONr_chiral_restr0.0520.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021321
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02226
LS refinement shellResolution: 2.502→2.566 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 57 -
Rwork0.283 367 -
all-424 -
obs--97.7 %
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)
12.28380.9298-0.62753.1333-3.45729.8604-0.27880.1848-0.14430.14690.1266-0.55-0.71780.40640.15230.3049-0.1325-0.01640.191-0.00670.154324.23849.72623.097
22.40231.24970.47173.13310.41245.5655-0.17550.0797-0.2869-0.04610.2085-0.3316-0.03530.3364-0.0330.1429-0.02710.02360.19630.02330.062517.13842.00526.889
30.80381.5189-0.80843.82650.25834.1505-0.0392-0.0613-0.3535-0.00130.0665-0.87190.19270.4086-0.02730.20280.0065-0.01430.22220.00860.208119.29940.70430.127
43.31312.90040.12075.609-0.4123.0718-0.10550.1103-0.39910.14780.1105-0.31780.2462-0.2517-0.0050.14560.0270.02540.17590.0230.05813.35638.07427.897
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 69
2X-RAY DIFFRACTION2A70 - 107
3X-RAY DIFFRACTION3A108 - 136
4X-RAY DIFFRACTION4A137 - 169

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