[English] 日本語
Yorodumi
- PDB-8d5i: Crystal structure of dihydropteroate synthase H182G mutant (folP-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d5i
TitleCrystal structure of dihydropteroate synthase H182G mutant (folP-SMZ_B27) from soil uncultured bacterium in complex with pteroic acid and pyrophosphate
ComponentsfolP-SMZ_B27
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / DIHYDROPTEROATE SYNTHASE / HYDROLASE / OXIDOREDUCTASE
Function / homologyPYROPHOSPHATE 2- / PTEROIC ACID
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsStogios, P.J. / Skarina, T. / Kim, Y. / Di Leo, R. / Venkatesan, M. / Savchenko, A. / Joachimiak, A. / 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)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of dihydropteroate synthase H182G mutant (folP-SMZ_B27) from soil uncultured bacterium in complex with pteroic acid
Authors: Stogios, P.J.
History
DepositionJun 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: folP-SMZ_B27
B: folP-SMZ_B27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5475
Polymers58,7472
Non-polymers8013
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-25 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.167, 145.614, 36.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11B-456-

HOH

21B-700-

HOH

-
Components

#1: Protein folP-SMZ_B27


Mass: 29373.408 Da / Num. of mol.: 2 / Mutation: H182G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold
#2: Chemical ChemComp-PT1 / PTEROIC ACID


Mass: 312.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 1% DMSO, 0.1 M Hepes pH 7.5, 5 mM para-aminobenzoic acid, 1.2 mM 6-hydroxymethyl-7,8-dihydropterin pyrophosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 42814 / % possible obs: 98.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.075 / Net I/σ(I): 16.5
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1703 / CC1/2: 0.982 / Rpim(I) all: 0.583 / % possible all: 79.5

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VIS

5vis


Resolution: 1.82→42.41 Å / SU ML: 0.2131 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1995 4.68 %RANDOM
Rwork0.1647 40624 --
obs0.1669 42619 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.99 Å2
Refinement stepCycle: LAST / Resolution: 1.82→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 55 580 4721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714226
X-RAY DIFFRACTIONf_angle_d0.94175737
X-RAY DIFFRACTIONf_chiral_restr0.0603666
X-RAY DIFFRACTIONf_plane_restr0.009748
X-RAY DIFFRACTIONf_dihedral_angle_d16.46851550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.34041140.32712315X-RAY DIFFRACTION78.76
1.86-1.910.32361380.26762789X-RAY DIFFRACTION96.06
1.91-1.960.25641410.23052870X-RAY DIFFRACTION98.46
1.96-2.030.27941440.2012904X-RAY DIFFRACTION99.32
2.03-2.10.24921440.18812917X-RAY DIFFRACTION99.58
2.1-2.180.25651420.18392901X-RAY DIFFRACTION99.15
2.18-2.280.25011450.17612963X-RAY DIFFRACTION99.78
2.28-2.40.27051420.16512902X-RAY DIFFRACTION99.67
2.4-2.550.23481450.16492973X-RAY DIFFRACTION99.9
2.55-2.750.21451450.15972926X-RAY DIFFRACTION99.35
2.75-3.030.20691450.16082995X-RAY DIFFRACTION99.78
3.03-3.470.20631460.14562971X-RAY DIFFRACTION99.33
3.47-4.360.15671480.13163024X-RAY DIFFRACTION99.56
4.37-42.410.18331560.1583174X-RAY DIFFRACTION98.84
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)
13.87143492748-4.124736696193.170135501697.88726804955-1.863378360694.98719274660.1436803923910.4109318154470.185431444502-0.729709670467-0.219152429340.6155228121350.0255383499275-0.330802366756-0.1046538481360.34258488806-0.05937159779570.02098982105230.281562464422-0.01148060662190.3275023875841.4255027609427.158752301213.0224678533
23.8486893224-2.065926018250.3280980714226.47807441229-1.207750439132.59643479772-0.05174559884430.108042965559-0.07768975519140.0788291903698-0.05973991243730.5862779273560.0230415291793-0.1549744907630.09051748623560.199583650053-0.0206402131791-0.0008105544700480.224400409788-0.06447398209940.2361525425120.93403288934129.009966842617.4025942371
34.882844750292.32431270636-3.970913668825.12434650667-3.17191780498.683628331190.0816360639111-0.08553317456420.1388013313440.2922101810370.04816699536190.0248267637013-0.156276001355-0.198233749318-0.1297764678220.1966836340270.0132527393857-0.0359761051070.207225984326-0.03831322206990.2321899611069.5047920827336.993135319818.6659286538
41.57238229101-0.26558259504-0.2754214731413.731800021592.787693325514.920910474260.04550468108840.06739552628870.0732276231991-0.04433769132240.0312500208165-0.169471652074-0.06074295325120.0827298627641-0.07920583553540.209165556758-0.01961223589090.004279190099880.1749275312780.03740072309470.22120557503421.013713093334.79940664718.68880391045
52.44652067250.6832455088440.4761385225864.261466385771.165032272482.768557846970.0264875514114-0.0337262896434-0.0621251387864-0.047771274837-0.0121578447982-0.2293606717270.0416812643020.0583813389421-0.01837990722130.1562174868210.02430206411320.02105175824740.1076963276380.01905737204320.13686224919718.69325380119.63815245526.8983022919
62.27452914948-2.6324673234-1.991781393618.80814882977-0.2397088231942.8605031556-0.0625048815151-0.607336314397-0.2901993045520.390941736020.160508845329-0.283174581110.1148040084820.199823595069-0.08902741006510.3419982999960.00735664748341-0.01136869444770.2247407908790.01359214046340.16481025389419.584915185510.315477437518.365178735
79.297930581425.97082738626-4.493493600745.349531463-4.088155788896.265172676220.240034276417-0.340786664777-0.2027035749220.234851285709-0.292183563274-0.1223214202820.2985516805610.009870141063510.04149684395680.2989488315410.01116022615060.02303309916680.170169570218-0.04965691150220.20498487513511.7487421546-11.41319187963.70412801485
89.550279266756.96856233092-4.105776322935.65525706769-4.541342685836.89901115063-0.0655887281652-0.447922470964-0.187113737085-0.00733425896608-0.1002780105780.4527406259940.349227174006-0.2382223824370.1082569165330.2019092666530.00143140001167-0.01830575055870.271643150726-0.05096792556270.255980201575.56389335588-13.4312830006-1.56162955881
91.94046668167-0.3946742053470.5047996090215.11456921451-1.724219692112.360763301790.100709007943-0.0460478937722-0.167622604212-0.06962597475530.05596677744610.09451502911310.05582577139160.0962100257032-0.1606166626340.1726366808840.000942862063890.01473083336580.236049905652-0.01755029962810.25337959956915.0085939342-18.06864350362.07820381159
105.552575745581.081406720252.15344438092.26070378191.754271199015.67880086036-0.04943779195920.107796181104-0.273223988766-0.1707562372570.119989460413-0.1449620728810.0687323977170.154348893912-0.06097258610020.1542474391140.002440771090560.0289018728430.129231800387-0.006917999000830.19757622947425.9710668339-18.2448485285-0.987196853152
112.70015954091-1.13265953371-0.9337674696592.353499033280.509495083041.96896777806-0.0870123697309-0.161228493513-0.04963647135450.2381256112510.0336836103434-0.07639708999120.038898114740.141296014670.04761948730510.205591846603-0.0192391003947-0.02848469496070.1843322313740.007449631726780.21641270326129.7101829361-5.658112123312.8314592455
124.20205509792-0.8404811082620.9921015263044.878242007661.376735976262.85517823546-0.05142085093340.1072808657240.112671847554-0.1704507622620.0625265804187-0.0546946917592-0.04859875425880.146122786952-0.003586469499080.1759374302940.00350591190233-7.84435779259E-60.1520723021990.00685669376780.14444950221620.48106283895.461477899963.37612379563
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 25 )AA1 - 251 - 25
22chain 'A' and (resid 26 through 77 )AA26 - 7726 - 77
33chain 'A' and (resid 78 through 115 )AA78 - 11578 - 115
44chain 'A' and (resid 116 through 187 )AA116 - 187116 - 187
55chain 'A' and (resid 188 through 252 )AA188 - 252188 - 252
66chain 'A' and (resid 253 through 270 )AA253 - 270253 - 270
77chain 'B' and (resid 1 through 21 )BC1 - 211 - 21
88chain 'B' and (resid 22 through 38 )BC22 - 3822 - 38
99chain 'B' and (resid 39 through 77 )BC39 - 7739 - 77
1010chain 'B' and (resid 78 through 130 )BC78 - 13078 - 130
1111chain 'B' and (resid 131 through 229 )BC131 - 229131 - 229
1212chain 'B' and (resid 230 through 270 )BC230 - 270230 - 270

+
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