[English] 日本語
Yorodumi
- PDB-6zaj: Room temperature XFEL Isopenicillin N synthase structure in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zaj
TitleRoom temperature XFEL Isopenicillin N synthase structure in complex with Fe, O2 and ACV after exposure to dioxygen for 3000ms.
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / Isopenicillin N synthase / oxygen binding / XFEL / time-resolved crystallography
Function / homology
Function and homology information


isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol
Similarity search - Function
Isopenicillin N synthase signature 1. / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE / : / OXYGEN MOLECULE / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.5301 Å
AuthorsRabe, P. / Kamps, J.J.A.G. / Sutherlin, K. / Pharm, C. / McDonough, M.A. / Leissing, T.M. / Aller, P. / Butryn, A. / Linyard, J. / Lang, P. ...Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K. / Pharm, C. / McDonough, M.A. / Leissing, T.M. / Aller, P. / Butryn, A. / Linyard, J. / Lang, P. / Brem, J. / Fuller, F.D. / Batyuk, A. / Hunter, M.S. / Pettinati, I. / Clifton, I.J. / Alonso-Mori, R. / Gul, S. / Young, I. / Kim, I. / Bhowmick, A. / ORiordan, L. / Brewster, A.S. / Claridge, T.D.W. / Sauter, N.K. / Yachandra, V. / Yano, J. / Kern, J.F. / Orville, A.M. / Schofield, C.J.
Funding support United Kingdom, United States, 13items
OrganizationGrant numberCountry
Wellcome Trust106244/Z/14/Z United Kingdom
Medical Research Council (MRC, United Kingdom)106244/Z/14/Z United Kingdom
Wellcome Trust210734/Z/18/Z United Kingdom
Royal SocietyRSWF/R2/182017 United Kingdom
Wellcome Trust102593 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)102593 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S50676X/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133081 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
Department of Energy (DOE, United States)DOE BES DE-AC02-05CH11231 United States
Department of Energy (DOE, United States)DOE BES DE-AC02-76SF00515 United States
CitationJournal: Sci Adv / Year: 2021
Title: X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis.
Authors: Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K.D. / Linyard, J.D.S. / Aller, P. / Pham, C.C. / Makita, H. / Clifton, I. / McDonough, M.A. / Leissing, T.M. / Shutin, D. / Lang, P.A. / Butryn, A. / ...Authors: Rabe, P. / Kamps, J.J.A.G. / Sutherlin, K.D. / Linyard, J.D.S. / Aller, P. / Pham, C.C. / Makita, H. / Clifton, I. / McDonough, M.A. / Leissing, T.M. / Shutin, D. / Lang, P.A. / Butryn, A. / Brem, J. / Gul, S. / Fuller, F.D. / Kim, I.S. / Cheah, M.H. / Fransson, T. / Bhowmick, A. / Young, I.D. / O'Riordan, L. / Brewster, A.S. / Pettinati, I. / Doyle, M. / Joti, Y. / Owada, S. / Tono, K. / Batyuk, A. / Hunter, M.S. / Alonso-Mori, R. / Bergmann, U. / Owen, R.L. / Sauter, N.K. / Claridge, T.D.W. / Robinson, C.V. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Orville, A.M. / Schofield, C.J.
History
DepositionJun 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: 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: Isopenicillin N synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1115
Polymers37,5641
Non-polymers5474
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-26 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.885, 75.639, 101.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Isopenicillin N synthase / / IPNS


Mass: 37563.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ipnA, ips, AN2622 / Production host: Escherichia coli (E. coli) / Strain (production host): NM 554 / References: UniProt: P05326, isopenicillin-N synthase

-
Non-polymers , 5 types, 167 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACV / L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE


Mass: 363.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.15 Å3/Da / Density % sol: 42.75 % / Description: needles - size range 40-60um x 3 um x 3 um
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.5 / Details: 1.7M Li2SO4, 0.1 M TRIS pH 8.5

-
Data collection

DiffractionMean temperature: 298 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.30179 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30179 Å / Relative weight: 1
ReflectionResolution: 1.53→21.13 Å / Num. obs: 49972 / % possible obs: 99.94 % / Redundancy: 90.71 % / Biso Wilson estimate: 22.1870954592 Å2 / CC1/2: 0.975 / R split: 0.16 / Net I/σ(I): 31.16
Reflection shellResolution: 1.53→1.556 Å / Redundancy: 22.48 % / Mean I/σ(I) obs: 0.679 / Num. unique obs: 2491 / CC1/2: 0.102 / R split: 1.113 / % possible all: 100
Serial crystallography sample deliveryDescription: acoustic droplet tape drive / Method: injection
Serial crystallography sample delivery injectionDescription: acoustic droplet tape drive

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
cctbx.xfeldata reduction
PHASERphasing
cxi.mergedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BLZ

1blz


Resolution: 1.5301→21.1283 Å / SU ML: 0.2187 / Cross valid method: THROUGHOUT / σ(F): 1.3317 / Phase error: 24.1983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 1999 4.0265 %
Rwork0.178 47647 -
obs0.1788 49646 99.9195 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.7271 Å2
Refinement stepCycle: LAST / Resolution: 1.5301→21.1283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 29 163 2773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009072753
X-RAY DIFFRACTIONf_angle_d0.931523764
X-RAY DIFFRACTIONf_chiral_restr0.05975396
X-RAY DIFFRACTIONf_plane_restr0.00664501
X-RAY DIFFRACTIONf_dihedral_angle_d9.233861622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5301-1.56830.37831420.36723367X-RAY DIFFRACTION99.5461
1.5683-1.61060.35361410.3483356X-RAY DIFFRACTION99.9428
1.6106-1.6580.3321390.32033318X-RAY DIFFRACTION99.9133
1.658-1.71150.27741390.30393350X-RAY DIFFRACTION99.9141
1.7115-1.77270.28941420.27673358X-RAY DIFFRACTION99.9144
1.7727-1.84360.27381420.25643393X-RAY DIFFRACTION99.887
1.8436-1.92740.26511430.22033381X-RAY DIFFRACTION99.9149
1.9274-2.0290.2181400.19173373X-RAY DIFFRACTION100
2.029-2.1560.19751430.17323398X-RAY DIFFRACTION100
2.156-2.32230.19221430.16093385X-RAY DIFFRACTION100
2.3223-2.55560.21561420.17423416X-RAY DIFFRACTION99.9719
2.5556-2.92460.20671450.17233448X-RAY DIFFRACTION100
2.9246-3.68150.18361450.14993463X-RAY DIFFRACTION100
3.6815-21.12830.13761530.13863641X-RAY DIFFRACTION99.8947
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)
12.93287041935-0.06059679137810.965685379497.477607872715.758041435368.88857362770.0242671843621-0.2368447525770.09905480484320.247441627686-0.08553316923050.05068219665270.021564994914-0.2996732459380.1081388699210.139650094381-0.03258898136640.03989273540330.2172959888390.05393801122150.149290344263-16.2461412522-2.6677423279715.7237765266
21.012757439440.596074762099-1.601774887390.88521320676-0.3804045024313.63788277916-0.003501854319660.2069904811950.167502687766-0.1696593136060.1697463414680.235732062179-0.256446362308-0.760802428268-0.2126447294140.181573254838-0.00526510380689-0.05319451728720.3081231795350.01669208384240.22891141301-22.69667135550.530494060007-1.92723534832
36.802348241880.469111904155-3.565807667634.698690890553.374942610357.595894619050.1266019995710.2633988360.36477021527-0.06882205754070.05378823685950.0431588483648-0.356092340090.0306240420883-0.1405724239630.267292757641-0.011274920309-0.02021984673690.2129265566760.04711808020670.165248398574-11.09767969526.60377025626-24.3679259555
41.991236032612.032914094870.5674561527537.471522849032.012402490313.70472199376-0.08734158785010.2252809711910.0497447319459-0.2881545496570.143587613918-0.0221180501805-0.3410902231320.170787442576-0.06104844249780.207101344846-0.001211611692820.009828134772250.2112395360920.0347909286650.163114093727-9.862631149526.40958174976-14.9517326913
57.032357249271.357327797920.7854012890133.103690591390.2257691285283.48663368129-0.01138928643880.5214061922670.140183499138-0.01824310986670.1101641480360.100023516842-0.9242784899540.0234945853008-0.01861118191660.424328026534-0.0006650484836080.04283277395540.2111766452870.06819462991760.182798623066-9.6076785905815.3982475336-13.1348615898
61.51630016202-1.30585954871.216880930123.29593571478-3.023936796567.380756069590.0224561565909-0.11097557270.1099779239540.0199750679150.0519066658252-0.058961870126-0.727990563416-0.0282125578903-0.03063090643560.249251864067-0.003999563072120.03574610729280.137822946896-0.02660096938820.180616260347-11.29705686199.660646748685.11434369121
71.21452719693-0.05436847114850.4298253001351.290024534630.0462425309822.3739833050.02345231051830.0403050306297-0.11258234041-0.08582013522190.0223508898380.02121550606130.06439715148330.0658790738608-0.04715466532020.122138742952-0.006440090676330.01061915224960.1578378177520.00881608684050.156379660264-11.2127694115-7.2661817372-3.34907260562
89.251296213985.79311568885-7.886744746328.01088495404-4.241251059136.975750701090.119966449678-0.689152832233-0.3345186291380.256881108691-0.2289466453740.02553278772840.3406178513321.860997313870.1522857488880.243871130608-0.00739516941666-0.05391005938580.5843944992290.01996947397990.3209221680737.25182551303-1.7131270030713.9697864397
98.220516757365.406147936.063273004594.90133968055.581772282357.34144249938-0.2608501807290.806435985336-0.427955456287-0.8868170515210.472035544029-0.1464092894020.05217861633210.803395635776-0.2441229363860.442346637956-0.00942562589690.02377394487210.4604222357270.0298430224460.3430809527790.692316177114-0.891453191898-8.52144587083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 182 )
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 295 )
8X-RAY DIFFRACTION8chain 'A' and (resid 296 through 312 )
9X-RAY DIFFRACTION9chain 'A' and (resid 313 through 331 )

+
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