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- PDB-7kp2: High Resolution Crystal Structure of Putative Pterin Binding Prot... -

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Entry
Database: PDB / ID: 7kp2
TitleHigh Resolution Crystal Structure of Putative Pterin Binding Protein (PruR) from Vibrio cholerae O1 biovar El Tor str. N16961 in Complex with Neopterin
ComponentsPutative Pterin Binding Protein
KeywordsPTERIN-BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / PruR / UNKNOWN FUNCTION / Pterin binding protein
Function / homologyOxidoreductase, molybdopterin-binding domain superfamily / L-NEOPTERIN / Oxidoreductase molybdopterin-binding domain-containing protein
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.03 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Dubrovska, I. / Endres, M. / 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: High Resolution Crystal Structure of Putative Pterin Binding Protein (PruR) from Vibrio cholerae O1 biovar El Tor str. N16961 in Complex with Neopterin.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Dubrovska, I. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 2.0Aug 17, 2022Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / chem_comp / entity / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly / pdbx_struct_sheet_hbond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_keywords / struct_mon_prot_cis
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.percent_reflns_obs / _software.version / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_mon_prot_cis.pdbx_omega_angle
Description: Ligand geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Putative Pterin Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9372
Polymers15,6841
Non-polymers2531
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.488, 54.616, 33.448
Angle α, β, γ (deg.)90.000, 91.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative Pterin Binding Protein


Mass: 15684.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_1933 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q9KQR5
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 8.8 mg/ml, 0.01M Tris pH 8.3, 2mM Neopterin; Screen: Classics II (D11), 0.1M Bis-Tris pH 6.5, 28% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2019 / Details: Be
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.03→30 Å / Num. obs: 57114 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.049 / Rrim(I) all: 0.105 / Rsym value: 0.092 / Χ2: 2.241 / Net I/σ(I): 22.1
Reflection shellResolution: 1.03→1.05 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2778 / CC1/2: 0.719 / CC star: 0.914 / Rpim(I) all: 0.404 / Rrim(I) all: 0.867 / Rsym value: 0.764 / Χ2: 1.007 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.03→21.48 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.68 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1467 2929 5.1 %RANDOM
Rwork0.1276 ---
obs0.1286 54176 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.92 Å2 / Biso mean: 10.534 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0.08 Å2
2---0.52 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 1.03→21.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1096 0 36 193 1325
Biso mean--12.21 24.13 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121458
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161301
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.6412020
X-RAY DIFFRACTIONr_angle_other_deg0.4171.5473067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7945189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.718105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.21910235
X-RAY DIFFRACTIONr_chiral_restr0.0650.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021703
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02275
X-RAY DIFFRACTIONr_rigid_bond_restr2.13532759
LS refinement shellResolution: 1.031→1.058 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 195 -
Rwork0.235 3772 -
all-3967 -
obs--90.99 %
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)
11.8293-4.9939-1.043613.63652.93593.8326-0.1837-0.09590.14170.50450.2594-0.38860.07470.1978-0.07580.04620.0016-0.04320.0739-0.02040.076825.35726.73120.317
20.81790.38740.21151.5319-0.2291.8361-0.05340.03480.00240.0220.0367-0.0529-0.15960.09350.01670.04170.00920.02420.0466-0.00540.047919.32730.8268.892
30.7304-0.76480.26271.6861-0.15440.8029-0.0266-0.038-0.00010.01670.0579-0.1731-0.0130.1094-0.03130.0113-0.00140.01350.0592-0.00150.047525.67725.5276.283
42.1160.3528-0.46271.87440.17563.8015-0.0043-0.0151-0.05090.21720.0021-0.07180.1691-0.01540.00220.063-0.00820.00820.03380.0070.014916.24316.58314.516
51.1401-0.312-0.36331.79130.42581.65970.010.0144-0.0039-0.0578-0.04850.0171-0.1407-0.07080.03850.01810.00040.00220.0353-0.00390.010317.03327.5798.116
60.21870.01040.09711.857-0.07811.4221-0.00780.0439-0.0116-0.14690.0133-0.04960.10290.0234-0.00550.0306-0.00320.01180.0517-0.00190.007116.06520.2555.154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 33
2X-RAY DIFFRACTION2A34 - 58
3X-RAY DIFFRACTION3A59 - 82
4X-RAY DIFFRACTION4A83 - 94
5X-RAY DIFFRACTION5A95 - 123
6X-RAY DIFFRACTION6A124 - 156

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