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- PDB-3tyz: Crystal Structure of the Yersinia pestis Dihydropteroate syntheta... -

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Basic information

Entry
Database: PDB / ID: 3tyz
TitleCrystal Structure of the Yersinia pestis Dihydropteroate synthetase with substrate transition state complex.
Components7,8-dihydropteroate synthase
KeywordsTRANSFERASE/TRANSFERASE SUBSTRATE / Dihydropteroate synthase / transition state complex / pABA / Tim barrel / TRANSFERASE-TRANSFERASE SUBSTRATE complex
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-AMINOBENZOIC ACID / PYROPHOSPHATE 2- / Chem-XHP / Dihydropteroate synthase / Dihydropteroate synthase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å
AuthorsWu, Y.
CitationJournal: Science / Year: 2012
Title: Catalysis and sulfa drug resistance in dihydropteroate synthase.
Authors: Yun, M.K. / Wu, Y. / Li, Z. / Zhao, Y. / Waddell, M.B. / Ferreira, A.M. / Lee, R.E. / Bashford, D. / White, S.W.
History
DepositionSep 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: 7,8-dihydropteroate synthase
B: 7,8-dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,66510
Polymers60,6352
Non-polymers1,0298
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-44 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.179, 50.522, 74.668
Angle α, β, γ (deg.)90.000, 90.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 7,8-dihydropteroate synthase / Dihydropteroate synthase


Mass: 30317.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: KIM D27 / Gene: dhpS, folP, y0683, YPO3501, YP_0582 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7CKJ1, UniProt: A0A2S9PLG4*PLUS, dihydropteroate synthase

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Non-polymers , 5 types, 263 molecules

#2: Chemical ChemComp-XHP / 2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one


Mass: 177.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N5O
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-PAB / 4-AMINOBENZOIC ACID


Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PEG 20,000, MES(pH6.5), pH 6-7, VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2011
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 31898 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.056 / Χ2: 0.906 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.07-2.113.60.29315061.077192.8
2.11-2.143.80.24915590.893199.4
2.14-2.1940.24115640.859198.2
2.19-2.234.10.21415730.915198.7
2.23-2.284.10.21616151.134199.4
2.28-2.334.20.16115691198.5
2.33-2.394.20.14415750.934199.6
2.39-2.454.20.12515830.872198.8
2.45-2.534.20.11215950.904198.8
2.53-2.614.20.10115960.8931100
2.61-2.74.20.09915900.985199.1
2.7-2.814.10.07516160.916199.4
2.81-2.944.20.06415810.8981100
2.94-3.094.20.05516110.89199.4
3.09-3.294.10.04616000.884199.6
3.29-3.544.20.04316100.988199.8
3.54-3.94.10.04716330.827199.7
3.9-4.464.10.0416000.763199.6
4.46-5.624.10.03116450.827199.7
5.62-5040.0216770.698199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.201 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1606 5 %RANDOM
Rwork0.194 ---
obs0.1957 31894 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.63 Å2 / Biso mean: 30.3874 Å2 / Biso min: 7.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å2-0 Å2-0.46 Å2
2--0.89 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 66 255 4444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214285
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9685831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1075559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19824.536183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81515692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1571525
X-RAY DIFFRACTIONr_chiral_restr0.080.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213253
X-RAY DIFFRACTIONr_mcbond_it0.2851.52756
X-RAY DIFFRACTIONr_mcangle_it0.5224408
X-RAY DIFFRACTIONr_scbond_it1.02731529
X-RAY DIFFRACTIONr_scangle_it1.6214.51418
LS refinement shellResolution: 2.07→2.123 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 110 -
Rwork0.216 2108 -
all-2218 -
obs--93.47 %
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)
11.76840.06040.47441.21610.69591.50960.0103-0.14450.09670.1343-0.0246-0.0516-0.0652-0.05380.01430.040.00370.01060.02020.01740.082817.653118.723839.6697
20.94610.1096-0.04791.02230.70112.40860.03320.3544-0.1728-0.22080.01360.02310.2247-0.1928-0.04680.1384-0.0033-0.01790.20460.00120.128616.2956-1.91487.1013
31.22812.9032-0.44426.8706-1.05060.16080.2733-0.16180.21310.4361-0.27640.494-0.06840.05480.00320.13230.00440.04960.18620.0150.214613.130713.807942.3851
43.12910.2795-1.79933.4006-0.89971.19890.03260.7078-0.2615-0.3104-0.188-0.27480.0453-0.35350.15540.20160.0655-0.04590.2416-0.06050.162623.3046-3.54077.9815
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 275
2X-RAY DIFFRACTION2B1 - 276
3X-RAY DIFFRACTION3A281
4X-RAY DIFFRACTION4B281

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