[English] 日本語
Yorodumi
- PDB-5usw: The crystal structure of 7,8-dihydropteroate synthase from Vibrio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5usw
TitleThe crystal structure of 7,8-dihydropteroate synthase from Vibrio fischeri ES114
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / 7 / 8-dihydropteroate synthase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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-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
ACETATE ION / FORMIC ACID / Dihydropteroate synthase
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.643 Å
AuthorsTan, K. / Zhou, M. / Anderson, W.F. / Joachimiak, A. / 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)HHSN272201200026C United States
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionFeb 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.7Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydropteroate synthase
B: Dihydropteroate synthase
C: Dihydropteroate synthase
D: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,39318
Polymers125,3214
Non-polymers1,07214
Water14,808822
1
A: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,36412
Polymers62,6602
Non-polymers70410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-31 kcal/mol
Surface area23740 Å2
MethodPISA
2
C: Dihydropteroate synthase
D: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0296
Polymers62,6602
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-26 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.953, 65.881, 94.942
Angle α, β, γ (deg.)90.00, 105.83, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase


Mass: 31330.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (strain ATCC 700601 / ES114) (bacteria)
Strain: ATCC 700601 / ES114 / Gene: folP, VF_0480 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)magic / References: UniProt: Q5E7M1, dihydropteroate synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium sodium tartrate, 20% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 8, 2017 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 130804 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.037 / Χ2: 0.586 / Net I/σ(I): 13.8
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6479 / Num. unique obs: 6479 / Rpim(I) all: 0.592 / Χ2: 0.812 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5JQ9

5jq9


Resolution: 1.643→36.13 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.48
RfactorNum. reflection% reflectionSelection details
Rfree0.204 6159 5 %random
Rwork0.1713 ---
obs0.1729 123109 92.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.643→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8301 0 70 822 9193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148738
X-RAY DIFFRACTIONf_angle_d1.26811823
X-RAY DIFFRACTIONf_dihedral_angle_d6.757345
X-RAY DIFFRACTIONf_chiral_restr0.0771382
X-RAY DIFFRACTIONf_plane_restr0.0081535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6426-1.66130.25351250.21462700X-RAY DIFFRACTION65
1.6613-1.68080.25831440.21373042X-RAY DIFFRACTION72
1.6808-1.70130.20911680.20553089X-RAY DIFFRACTION74
1.7013-1.72290.23481730.19973298X-RAY DIFFRACTION79
1.7229-1.74550.23581640.21723501X-RAY DIFFRACTION83
1.7455-1.76940.25411800.2063511X-RAY DIFFRACTION84
1.7694-1.79470.26951820.20493605X-RAY DIFFRACTION86
1.7947-1.82150.25921970.19493732X-RAY DIFFRACTION89
1.8215-1.850.23222160.18763785X-RAY DIFFRACTION91
1.85-1.88030.20592020.1883913X-RAY DIFFRACTION93
1.8803-1.91270.21352020.18913986X-RAY DIFFRACTION95
1.9127-1.94750.19772060.18794073X-RAY DIFFRACTION97
1.9475-1.98490.23161880.18074164X-RAY DIFFRACTION98
1.9849-2.02550.20831950.18334135X-RAY DIFFRACTION99
2.0255-2.06950.20452100.18664120X-RAY DIFFRACTION98
2.0695-2.11760.2122190.17814111X-RAY DIFFRACTION98
2.1176-2.17060.20812170.17124066X-RAY DIFFRACTION97
2.1706-2.22930.21292400.16744149X-RAY DIFFRACTION99
2.2293-2.29480.2151930.16594212X-RAY DIFFRACTION99
2.2948-2.36890.21662270.16354197X-RAY DIFFRACTION99
2.3689-2.45350.18212330.16394165X-RAY DIFFRACTION99
2.4535-2.55180.20732420.16684173X-RAY DIFFRACTION100
2.5518-2.66790.2162440.17084153X-RAY DIFFRACTION100
2.6679-2.80850.22992380.17454182X-RAY DIFFRACTION99
2.8085-2.98430.21192320.174143X-RAY DIFFRACTION98
2.9843-3.21460.19612150.16884090X-RAY DIFFRACTION97
3.2146-3.53790.17142430.14754193X-RAY DIFFRACTION99
3.5379-4.04920.17792250.14574174X-RAY DIFFRACTION99
4.0492-5.09930.15172220.14244186X-RAY DIFFRACTION98
5.0993-36.13850.22512170.18824102X-RAY DIFFRACTION94
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)
10.4024-0.31870.15650.90350.12240.2705-0.0419-0.0310.05930.04970.0348-0.0418-0.0220.01330.00120.10690.00770.01430.15430.00580.067752.095151.148555.0885
22.3208-0.6803-0.83592.3233-1.47411.6954-0.0116-0.04510.0597-0.05410.0128-0.47380.09970.391-0.09390.12490.0160.00280.2397-0.01340.166771.454620.810649.2356
32.517-1.9870.28171.92960.82643.05230.13420.1704-0.2551-0.3092-0.25390.10880.196-0.3301-0.01160.1811-0.01760.04060.25-0.01750.186467.794618.471539.1828
44.43120.3883-2.43486.1899-1.6043.5471-0.24060.2505-0.225-0.68120.1411-0.00360.3930.01620.08350.17410.00930.02890.2145-0.00930.121773.21269.807842.1356
51.617-0.235-0.58530.54760.58490.6863-0.14-0.1301-0.19780.0690.07520.03230.11880.10440.05870.13520.02580.02060.16730.03470.09856.935817.016555.4551
64.6671.31413.22157.20695.47677.66520.0477-0.01770.0450.0963-0.0013-0.33310.02960.0465-0.02370.05890.0014-0.00630.10330.04580.141364.989635.962351.7212
71.2836-0.42790.04161.00970.43560.44770.00880.0379-0.0832-0.01740.0080.1206-0.0011-0.0642-0.05410.0894-0.01720.00080.06860.01270.093929.132120.20788.0095
80.4894-0.8213-0.09861.812-0.51011.77540.12050.08260.1043-0.0958-0.0585-0.1874-0.21020.3192-0.05980.1079-0.03450.02820.11860.01690.09633.693121.67179.4141
91.2454-0.1070.73251.97520.61582.4938-0.02060.09560.1521-0.0983-0.037-0.0159-0.16620.01230.04410.07210.01250.01670.0450.00570.09428.797430.309289.3549
105.4653-3.78452.22553.4239-1.35061.3894-0.3848-0.10420.22160.4250.1648-0.0961-0.23890.04850.19820.1607-0.012-0.0090.1108-0.02630.111843.111426.5033110.8835
110.8733-0.29590.34761.38870.28930.2951-0.01890.02060.05810.05540.0258-0.0051-0.04850.0254-0.01530.0869-0.00830.02330.04410.01590.060340.101213.157298.3058
123.1414-1.0564-1.18672.5841-1.02342.4361-0.0327-0.1611-0.203-0.0217-0.0727-0.1315-0.08160.25410.0090.0674-0.02010.0040.09570.02740.12157.921-11.091795.2324
131.0921-0.190.8821.51671.05111.79850.07120.2366-0.2415-0.1072-0.18220.09880.1808-0.12890.0510.1217-0.00250.03790.1606-0.05420.130854.0896-13.77184.7576
141.43970.1982-0.85011.8-0.83042.0057-0.14830.0339-0.4554-0.140.0058-0.07940.26450.09880.06290.10390.01910.0360.0710.01420.192857.8348-23.221992.2487
154.0368-2.9747-0.09343.04030.02520.7713-0.2251-0.0654-0.35120.27020.01980.0820.11510.03930.17230.1255-0.0130.03210.09610.06130.156339.0355-20.3387109.327
161.5031-0.1436-0.13611.2108-0.18310.27290.0081-0.0033-0.06250.0306-0.008-0.0150.03810.0141-0.01030.0745-0.00510.01150.04020.01510.059244.3628-6.421497.9626
171.41370.2864-1.06721.8653-1.35074.24270.0697-0.03740.0142-0.0472-0.07990.0191-0.08560.09170.01970.0768-0.0036-0.00360.120.00480.078942.825951.861539.292
182.23620.45691.47624.33970.81983.5894-0.0360.04210.1461-0.2305-0.0775-0.0149-0.293-0.09350.09650.11140.0480.0080.12150.00730.05539.955360.990739.3395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 110 through 278 )
2X-RAY DIFFRACTION2chain 'D' and (resid 0 through 36 )
3X-RAY DIFFRACTION3chain 'D' and (resid 37 through 70 )
4X-RAY DIFFRACTION4chain 'D' and (resid 71 through 109 )
5X-RAY DIFFRACTION5chain 'D' and (resid 110 through 258 )
6X-RAY DIFFRACTION6chain 'D' and (resid 259 through 277 )
7X-RAY DIFFRACTION7chain 'A' and (resid 0 through 33 )
8X-RAY DIFFRACTION8chain 'A' and (resid 34 through 70 )
9X-RAY DIFFRACTION9chain 'A' and (resid 71 through 139 )
10X-RAY DIFFRACTION10chain 'A' and (resid 140 through 175 )
11X-RAY DIFFRACTION11chain 'A' and (resid 176 through 278 )
12X-RAY DIFFRACTION12chain 'B' and (resid 0 through 36 )
13X-RAY DIFFRACTION13chain 'B' and (resid 37 through 70 )
14X-RAY DIFFRACTION14chain 'B' and (resid 71 through 139 )
15X-RAY DIFFRACTION15chain 'B' and (resid 140 through 175 )
16X-RAY DIFFRACTION16chain 'B' and (resid 176 through 277 )
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 70 )
18X-RAY DIFFRACTION18chain 'C' and (resid 71 through 109 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more