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- PDB-5vis: 1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Syn... -

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Entry
Database: PDB / ID: 5vis
Title1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Synthase (folP-SMZ_B27) from Soil Uncultured Bacterium.
ComponentsDihydropteroate Synthase
KeywordsHYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Dihydropteroate Synthase
Function / homologyDihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / : / MALONIC ACID / D(-)-TARTARIC ACID
Function and homology information
Biological speciessoil metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsMinasov, G. / Wawrzak, Z. / Di Leo, R. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.73 Angstrom Resolution Crystal Structure of Dihydropteroate Synthase (folP-SMZ_B27) from Soil Uncultured Bacterium.
Authors: Minasov, G. / Wawrzak, Z. / Di Leo, R. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_special_symmetry
Revision 1.2Apr 3, 2019Group: Data collection / Other / Structure summary / Category: audit_author / pdbx_SG_project / struct_keywords
Item: _pdbx_SG_project.full_name_of_center / _pdbx_SG_project.initial_of_center / _struct_keywords.text
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydropteroate Synthase
B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8747
Polymers59,4542
Non-polymers4215
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 1AJ2
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-13 kcal/mol
Surface area23470 Å2
MethodPISA
2
A: Dihydropteroate Synthase
B: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
B: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
B: Dihydropteroate Synthase
hetero molecules

A: Dihydropteroate Synthase
B: Dihydropteroate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,49728
Polymers237,8148
Non-polymers1,68320
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_556-x+y,y,-z+11
Buried area26560 Å2
ΔGint-151 kcal/mol
Surface area77620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.822, 101.822, 206.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-301-

CL

21A-657-

HOH

31B-533-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydropteroate Synthase


Mass: 29726.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) soil metagenome (others) / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 Gold

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Non-polymers , 6 types, 635 molecules

#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.2 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 30.0 mg/ml, 0.25M Sodium chloride, 0.25M Potassium chloride, 0.01M HEPES (pH 7.5); Screen: 0.2M Potassium citrate, 0.1M MES (pH 6.5), 20% (w/v) PEG 3350; Cryo: 5% (v/v) PEG 200, paratone.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. obs: 66663 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Rsym value: 0.072 / Χ2: 1.027 / Net I/σ(I): 20.7
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3260 / CC1/2: 0.737 / Rpim(I) all: 0.325 / Rsym value: 0.752 / Χ2: 1.032 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AJ2

1aj2


Resolution: 1.73→29.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.612 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19091 3346 5 %RANDOM
Rwork0.15661 ---
obs0.1583 63061 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.277 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å20 Å2
2---0.23 Å20 Å2
3---0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.73→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 25 630 4768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194456
X-RAY DIFFRACTIONr_bond_other_d0.0010.024244
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9746068
X-RAY DIFFRACTIONr_angle_other_deg0.87939831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6455592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24923.505194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.30215769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2791542
X-RAY DIFFRACTIONr_chiral_restr0.0940.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0215133
X-RAY DIFFRACTIONr_gen_planes_other0.020.02901
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1581.4082299
X-RAY DIFFRACTIONr_mcbond_other1.1561.4072298
X-RAY DIFFRACTIONr_mcangle_it1.9152.0982914
X-RAY DIFFRACTIONr_mcangle_other1.9152.12915
X-RAY DIFFRACTIONr_scbond_it1.6311.6682157
X-RAY DIFFRACTIONr_scbond_other1.6291.6672157
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6072.4223155
X-RAY DIFFRACTIONr_long_range_B_refined6.18819.7175278
X-RAY DIFFRACTIONr_long_range_B_other5.83618.3475072
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 243 -
Rwork0.237 4548 -
obs--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)
18.5121-7.6487-1.76159.21891.89561.6541-0.0469-0.17840.00340.02810.08550.12910.0297-0.052-0.03850.05550.0203-0.01570.06540.00320.029525.27386.7411119.2775
21.445-0.1201-0.63691.21890.45351.8674-0.08330.04950.11420.11460.01510.2196-0.1527-0.3370.06820.1180.08130.00530.1994-0.0010.075316.205512.6649122.3374
30.8710.1782-0.15750.965-0.36540.88940.0057-0.18160.07610.21480.0206-0.062-0.13370.105-0.02630.10290.0295-0.03370.077-0.01930.044632.678516.4524118.1228
41.56540.2067-0.01761.34670.22951.1408-0.0618-0.0744-0.15630.10220.0574-0.09350.10750.07010.00450.05260.0242-0.01030.0260.0080.027932.1828-1.6175110.9116
58.6181-8.1434-2.11538.34381.58111.7662-0.00180.2539-0.11250.022-0.10110.11680.1166-0.17160.10290.0786-0.01880.00210.0676-0.0050.03753.807225.26786.9658
69.3226-2.7533-4.03625.23292.52276.2239-0.0773-0.0964-0.4154-0.0584-0.0215-0.33750.66450.37350.09880.24370.04780.06530.04540.00070.08989.0859.532581.4057
70.77480.47970.42781.05180.80861.307-0.06980.1225-0.0429-0.17930.084-0.0845-0.04460.0912-0.01430.052-0.01210.02130.05230.00610.015316.493330.187284.0747
81.16490.0944-0.68220.7299-0.04981.9167-0.0930.0017-0.02050.0030.01910.02810.15230.01570.07390.0250.00770.00650.01930.0010.00414.30729.56697.2285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 17
2X-RAY DIFFRACTION2A18 - 57
3X-RAY DIFFRACTION3A58 - 233
4X-RAY DIFFRACTION4A234 - 272
5X-RAY DIFFRACTION5B-1 - 21
6X-RAY DIFFRACTION6B22 - 36
7X-RAY DIFFRACTION7B37 - 195
8X-RAY DIFFRACTION8B196 - 271

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