[English] 日本語
Yorodumi
- PDB-6xqx: Crystal structure of the catalytic domain of PBP2 S310A from Neis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xqx
TitleCrystal structure of the catalytic domain of PBP2 S310A from Neisseria gonorrhoeae with the H514A mutation at pH 7.5
ComponentsProbable peptidoglycan D,D-transpeptidase PenA
KeywordsHYDROLASE / PBP2 / beta-lactam / antibiotic target
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic ...peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Probable peptidoglycan D,D-transpeptidase PenA
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFenton, B.A. / Zhou, P. / Davies, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066861 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Mutations in PBP2 from ceftriaxone-resistant Neisseria gonorrhoeae alter the dynamics of the beta 3-beta 4 loop to favor a low-affinity drug-binding state.
Authors: Fenton, B.A. / Tomberg, J. / Sciandra, C.A. / Nicholas, R.A. / Davies, C. / Zhou, P.
History
DepositionJul 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable peptidoglycan D,D-transpeptidase PenA
B: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8418
Polymers70,4342
Non-polymers4066
Water1,26170
1
A: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3753
Polymers35,2171
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable peptidoglycan D,D-transpeptidase PenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4655
Polymers35,2171
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.520, 77.310, 88.180
Angle α, β, γ (deg.)90.000, 91.623, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPROPRO(chain 'A' and (resid 237 through 304 or resid 306...AA237 - 2823 - 48
12GLYGLYASPASP(chain 'A' and (resid 237 through 304 or resid 306...AA296 - 30449 - 57
13ILEILEVALVAL(chain 'A' and (resid 237 through 304 or resid 306...AA306 - 34459 - 97
14ASPASPLYSLYS(chain 'A' and (resid 237 through 304 or resid 306...AA346 - 36199 - 114
15SERSERTYRTYR(chain 'A' and (resid 237 through 304 or resid 306...AA363 - 383116 - 136
16GLUGLUVALVAL(chain 'A' and (resid 237 through 304 or resid 306...AA385 - 489138 - 242
17GLYGLYLYSLYS(chain 'A' and (resid 237 through 304 or resid 306...AA491 - 503244 - 256
18VALVALVALVAL(chain 'A' and (resid 237 through 304 or resid 306...AA505258
19TYRTYRTHRTHR(chain 'A' and (resid 237 through 304 or resid 306...AA509 - 573262 - 326
21LEULEUPROPRO(chain 'B' and (resid 237 through 304 or resid 306...BB237 - 2823 - 48
22GLYGLYASPASP(chain 'B' and (resid 237 through 304 or resid 306...BB296 - 30449 - 57
23ILEILEVALVAL(chain 'B' and (resid 237 through 304 or resid 306...BB306 - 34459 - 97
24ASPASPLYSLYS(chain 'B' and (resid 237 through 304 or resid 306...BB346 - 36199 - 114
25SERSERTYRTYR(chain 'B' and (resid 237 through 304 or resid 306...BB363 - 383116 - 136
26GLUGLUVALVAL(chain 'B' and (resid 237 through 304 or resid 306...BB385 - 489138 - 242
27GLYGLYLYSLYS(chain 'B' and (resid 237 through 304 or resid 306...BB491 - 503244 - 256
28VALVALVALVAL(chain 'B' and (resid 237 through 304 or resid 306...BB505258
29TYRTYRTHRTHR(chain 'B' and (resid 237 through 304 or resid 306...BB509 - 573262 - 326

-
Components

#1: Protein Probable peptidoglycan D,D-transpeptidase PenA / Penicillin-binding protein 2 / PBP-2


Mass: 35217.219 Da / Num. of mol.: 2 / Mutation: S310A, H514A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: penA / Production host: Escherichia coli (E. coli)
References: UniProt: P08149, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 15% PEG 1500, 0.062 M Tris pH 7.5, 50 mM KCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→44.5 Å / Num. obs: 31251 / % possible obs: 95.6 % / Redundancy: 5.6 % / Biso Wilson estimate: 44.91 Å2 / Rrim(I) all: 0.133 / Net I/σ(I): 7.07
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.16 / Num. unique obs: 3231 / Rrim(I) all: 0.389 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER1.17.1_3660phasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P53

6p53


Resolution: 2.15→44.5 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 29.4905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 1559 5 %
Rwork0.2158 29644 -
obs0.2172 31203 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.07 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4904 0 25 70 4999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225077
X-RAY DIFFRACTIONf_angle_d0.61386880
X-RAY DIFFRACTIONf_chiral_restr0.0434769
X-RAY DIFFRACTIONf_plane_restr0.0037898
X-RAY DIFFRACTIONf_dihedral_angle_d20.08661879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.220.31641450.29252780X-RAY DIFFRACTION97.86
2.22-2.30.31941430.27122698X-RAY DIFFRACTION97.6
2.3-2.390.33541400.27312658X-RAY DIFFRACTION94.88
2.39-2.50.28861450.26732752X-RAY DIFFRACTION98
2.5-2.630.32071430.25662776X-RAY DIFFRACTION98.45
2.63-2.80.28631450.27092737X-RAY DIFFRACTION97.4
2.8-3.010.32061430.25522712X-RAY DIFFRACTION96.88
3.01-3.320.26641410.25452674X-RAY DIFFRACTION95.33
3.32-3.790.25541330.22432530X-RAY DIFFRACTION89.6
3.79-4.780.19171410.17832687X-RAY DIFFRACTION94.39
4.78-44.50.18621400.16352640X-RAY DIFFRACTION91.33
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)
11.157799969030.6041057198130.07092555795920.465326077427-0.1655274004750.7050322274590.333236694213-0.5396029972220.008760259406451.36128524779-0.360604711283-0.291086582583-0.508134520685-0.1049772873140.003127192117210.996541984777-0.172547271597-0.1830675927870.5441209833140.06061920320240.400309339146-9.27035888983-23.63252774025.37273695415
20.9756319136421.05184490770.1937740611153.149577126430.5034676600071.849392831570.06026378651770.003980561457440.02576991116960.38246911321-0.02863738959650.1008489988660.09040331619590.02303811262540.0003229704165730.4263741080470.01638747973540.0004525947512890.332594674035-0.004639585384720.319482086123-19.2114800527-25.4740923317-14.8195519858
31.631835740211.400078274630.2081691727771.7474430984-0.5719160804791.20220963260.336514889281-0.243399719878-0.1674636735621.12011868616-0.3340893922990.300515400762-0.119015845812-0.02064990467580.003813186906360.870284601881-0.09139705619560.1236565799140.402882863779-0.005306917290420.444654689952-22.442375733-27.37244366331.58439141469
40.564313944252-0.548818008582-0.1489657237410.6310782918550.4318484474260.8550875848180.2001931571880.0325866084301-0.072823156836-0.597912411686-0.281875926846-0.2309609194090.1272230226740.242667101717-0.0004334110103420.673377128150.0661432726580.1357457199590.6448096848520.08270868281040.43794080652-0.305585237205-14.5272267129-50.4798749714
51.552109844430.880771290669-0.3819784329091.84577009167-0.7062872227082.399878536260.0686508497696-0.1108318720340.1320647492320.0672361156081-0.017106974144-0.130931275661-0.1880526105840.36775210199-0.0001138120816980.322089820545-0.0720112324408-0.01758088691550.453214615465-0.01404250035070.397704673599-6.12852653338-3.83907095217-29.0808862974
60.479376374050.1999946437110.02455700286010.236794412171-0.1925033690570.2646195022320.06564310470170.740594101954-0.0116651033333-0.323626437269-0.1298076130650.01078272110350.575468902364-0.6335810348630.000771859702240.563890698061-0.0651397460295-0.01398049224920.495814630728-0.04145688059180.333356258331-16.987834417-19.2326951023-38.2442935385
70.7299130104380.220236310041-0.5784407240692.244483612920.1333417136041.340787114370.04928802455370.2493190860470.287814202645-0.36334515541-0.0285316678-0.0741067960956-0.01054946404240.184171355793-0.0008321519358450.381809280739-0.02399721841410.03172140786210.4541711831450.09253806822350.392108193972-5.55263250164-3.89547325362-41.7029772033
80.308890617636-0.280771773079-0.1327245380350.943541267857-0.3291002658590.3383031229740.13748834638-0.09329710766660.544136368561-0.488360866508-0.0894757046364-0.207774037206-0.1554192241960.0917065581593.15352265458E-50.55839323876-0.02406224502920.06684992715350.614077805320.06979644541990.552355074568-3.91919700593-3.43951626675-52.6808650034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 236 through 308 )
2X-RAY DIFFRACTION2chain 'A' and (resid 309 through 463 )
3X-RAY DIFFRACTION3chain 'A' and (resid 464 through 573 )
4X-RAY DIFFRACTION4chain 'B' and (resid 237 through 281 )
5X-RAY DIFFRACTION5chain 'B' and (resid 282 through 439 )
6X-RAY DIFFRACTION6chain 'B' and (resid 440 through 463 )
7X-RAY DIFFRACTION7chain 'B' and (resid 464 through 536 )
8X-RAY DIFFRACTION8chain 'B' and (resid 537 through 574 )

+
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