[English] 日本語
Yorodumi
- PDB-6ucz: Crystal structure of dihydropteroate synthase from Anaplasma phag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ucz
TitleCrystal structure of dihydropteroate synthase from Anaplasma phagocytophilum with bound 6-hydroxymethylpterin-monophosphate
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / SSGCID / PMM / dihydropteroate synthase / ptp / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding
Similarity search - Function
Dihydropteroate synthase signature 1. / 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
ACETATE ION / CITRIC ACID / PTERIN-6-YL-METHYL-MONOPHOSPHATE / Dihydropteroate synthase
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of dihydropteroate synthase from Anaplasma phagocytophilum with bound 6-hydroxymethylpterin-monophosphate
Authors: Bolejack, M.J. / Delker, S.L. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Mar 11, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,81812
Polymers63,8432
Non-polymers97410
Water4,720262
1
A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4695
Polymers31,9221
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3497
Polymers31,9221
Non-polymers4276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.830, 81.480, 71.170
Angle α, β, γ (deg.)90.000, 102.670, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Dihydropteroate synthase / / DHPS / Dihydropteroate pyrophosphorylase


Mass: 31921.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Gene: WSQ_01200, folP / Plasmid: AnphA.01019.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S5PWL8, dihydropteroate synthase

-
Non-polymers , 6 types, 272 molecules

#2: Chemical ChemComp-PMM / PTERIN-6-YL-METHYL-MONOPHOSPHATE


Mass: 273.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N5O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1:1 20 mg/mL AnphA.01019.a.A1.PW27052 in 2.5 mM Ptp, 100 mM sodium cacodylate/HCl, pH 6.5, 20% w/v PEG8000, 200 mM magnesium acetate against 100 mM sodium citrate tribasic/HCl, pH 5.5, 20% ...Details: 1:1 20 mg/mL AnphA.01019.a.A1.PW27052 in 2.5 mM Ptp, 100 mM sodium cacodylate/HCl, pH 6.5, 20% w/v PEG8000, 200 mM magnesium acetate against 100 mM sodium citrate tribasic/HCl, pH 5.5, 20% w/v PEG3000, cryoprotectant: 20% ethylene glycol, 2.5 mM Ptp, tray 311087h9, puck tni6-6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 25, 2019 / Details: Beryllium Lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→38.75 Å / Num. obs: 36233 / % possible obs: 98.2 % / Redundancy: 3.659 % / Biso Wilson estimate: 34.394 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.052 / Χ2: 1.023 / Net I/σ(I): 19.42 / Num. measured all: 132591 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.052.7150.3422.916218272222900.9120.42584.1
2.05-2.112.9820.26347457264725010.9540.31994.5
2.11-2.173.5060.254.798940255325500.9630.29699.9
2.17-2.243.8170.2196.129481249424840.9770.25699.6
2.24-2.313.8170.1737.469320243924420.9850.201100
2.31-2.393.8240.148.998910233223300.990.16399.9
2.39-2.483.8180.12110.298599225822520.9910.14199.7
2.48-2.583.8280.09812.388407220321960.9950.11499.7
2.58-2.73.8320.07915.278012208720910.9960.092100
2.7-2.833.8230.0717.757603199619890.9960.08299.6
2.83-2.983.8150.05721.167256190719020.9970.06699.7
2.98-3.163.8120.04625.586865180518010.9980.05399.8
3.16-3.383.8120.03432.346485170317010.9990.0499.9
3.38-3.653.8130.0336.985975157015670.9990.03599.8
3.65-43.7810.02544.445532147014630.9990.02999.5
4-4.473.7870.02149.124995132413190.9990.02599.6
4.47-5.163.8090.0251.84407115711570.9990.023100
5.16-6.323.7760.02249.0837579979950.9990.02599.8
6.32-8.943.7040.01952.228527737700.9990.02299.6
8.94-38.753.510.01656.9515204434330.9990.01997.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OMZ

6omz


Resolution: 2→38.75 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.74
RfactorNum. reflection% reflection
Rfree0.1975 1985 5.48 %
Rwork0.1619 --
obs0.1639 36196 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.7 Å2 / Biso mean: 39.8793 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 2→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 66 270 4268
Biso mean--49.73 45.45 -
Num. residues----519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.26861080.23292100220884
2.05-2.110.24441200.20832325244594
2.11-2.170.19921420.193824632605100
2.17-2.240.24491550.181524502605100
2.24-2.320.25111430.171225112654100
2.32-2.410.21571240.168824652589100
2.41-2.520.21031480.165224622610100
2.52-2.650.20291490.167424842633100
2.65-2.820.22291490.168224692618100
2.82-3.040.19981460.171824832629100
3.04-3.340.1921530.157724692622100
3.34-3.820.18011710.143624752646100
3.82-4.820.17431410.138525042645100
4.82-38.750.17841360.160725512687100
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)
13.6360.9146-0.41813.22210.01496.78920.0937-0.26410.25380.239-0.1-0.2321-0.35270.50670.02050.4015-0.0324-0.03890.2349-0.06920.271524.859727.1642-26.9831
21.5460.1193-0.72352.7273-0.05644.8504-0.0146-0.1324-0.0014-0.0338-0.04430.18370.1292-0.18820.070.231-0.0236-0.00330.1918-0.02520.166514.875413.2724-32.4126
37.1179-2.1746-5.04264.1091.71769.26130.03190.08710.14210.1750.0282-0.6735-0.24160.8739-0.08980.4119-0.0643-0.05920.28060.00740.240519.60511.01822.3217
42.6537-0.07990.15261.9783-0.27223.68460.02670.12780.0531-0.05560.01660.08790.0080.1546-0.07550.36850.01350.01780.1625-0.00730.15659.139-2.6175-5.6098
51.7759-0.19840.99325.39723.22424.1567-0.10150.10310.1726-0.4989-0.23030.5409-0.5055-0.25860.27860.343-0.0007-0.00910.2093-0.01790.2076-7.54189.4861-1.033
62.4354-0.01580.91560.61030.78953.6709-0.0267-0.02540.15370.264-0.02130.08380.05-0.02240.04670.43140.00770.03260.1547-0.00190.19152.48078.164412.6091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 142 )A28 - 142
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 292 )A143 - 292
3X-RAY DIFFRACTION3chain 'B' and (resid 28 through 64 )B28 - 64
4X-RAY DIFFRACTION4chain 'B' and (resid 65 through 157 )B65 - 157
5X-RAY DIFFRACTION5chain 'B' and (resid 158 through 222 )B158 - 222
6X-RAY DIFFRACTION6chain 'B' and (resid 223 through 292 )B223 - 292

+
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