[English] 日本語
Yorodumi
- PDB-7r1k: Phosphorylated Bacillus pumilus Lipase A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r1k
TitlePhosphorylated Bacillus pumilus Lipase A
ComponentsLipase
KeywordsHYDROLASE / lipase / esterase / intermediate / complex
Function / homologyLipase EstA/Esterase EstB / Lipase (class 2) / lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / DIETHYL PHOSPHONATE / OXALOACETATE ION / Lipase
Function and homology information
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLund, B.A.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway262695 Norway
Research Council of Norway274858 Norway
CitationJournal: Biochemistry / Year: 2022
Title: Structure and Mechanism of a Cold-Adapted Bacterial Lipase
Authors: Lund, B.A. / Svalberg, L. / Purg, M. / Chukwu, G. / Widersten, M. / Isaksen, G.V. / Brandsdal, B.O. / Aqvist, J.
History
DepositionFeb 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7523
Polymers20,4831
Non-polymers2692
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint6 kcal/mol
Surface area7850 Å2
Unit cell
Length a, b, c (Å)57.396, 42.843, 62.660
Angle α, β, γ (deg.)90.000, 91.280, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

-
Components

#1: Protein Lipase


Mass: 20483.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: L5 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Nico21(DE3) / References: UniProt: W8FKE7
#2: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5 18-22 % PEG 4000 0.1-0.5 M lithium citrate 1:100 diluted paraoxon-ethyl mixed with enzyme
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 298 K / Ambient temp details: room temperature / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→20.93 Å / Num. obs: 47178 / % possible obs: 98.68 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.89 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.05036 / Net I/σ(I): 9.42
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.492 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 4727 / CC1/2: 0.399 / Rpim(I) all: 0.8465 / % possible all: 98.51

-
Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
APEX 2data collection
Aimless0.7.3data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1isp

1isp


Resolution: 1.5→20.93 Å / SU ML: 0.1767 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.4494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1652 2291 4.86 %
Rwork0.1408 44856 -
obs0.1419 47147 98.72 %
Solvent computationShrinkage radii: 0.4 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.56 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 17 99 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821440
X-RAY DIFFRACTIONf_angle_d0.87291949
X-RAY DIFFRACTIONf_chiral_restr0.0595217
X-RAY DIFFRACTIONf_plane_restr0.0097258
X-RAY DIFFRACTIONf_dihedral_angle_d15.4366522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.31541370.31052746X-RAY DIFFRACTION98.26
1.53-1.570.29931800.27392797X-RAY DIFFRACTION99.23
1.57-1.610.24171300.24932809X-RAY DIFFRACTION98.96
1.61-1.650.26591730.2342844X-RAY DIFFRACTION99.34
1.65-1.70.25141500.21112783X-RAY DIFFRACTION99.32
1.7-1.750.23951410.19282814X-RAY DIFFRACTION99.56
1.75-1.820.19791480.17482831X-RAY DIFFRACTION99.67
1.82-1.890.1721240.14062894X-RAY DIFFRACTION99.93
1.89-1.980.17221540.12312803X-RAY DIFFRACTION99.93
1.98-2.080.15641590.11482814X-RAY DIFFRACTION99.33
2.08-2.210.15941490.11422848X-RAY DIFFRACTION99.8
2.21-2.380.11731460.10072829X-RAY DIFFRACTION99.07
2.38-2.620.17031080.1172738X-RAY DIFFRACTION95.79
2.62-30.11041300.1162839X-RAY DIFFRACTION99.16
3-3.770.12611610.11322776X-RAY DIFFRACTION99.16
3.77-20.930.13621010.12762691X-RAY DIFFRACTION93.07
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)
13.70271174361-3.974600869860.7459165426268.49654899536-3.27367576373.182380906760.08909672796460.0466816862177-0.223274319923-0.01132559033810.03590477105740.421154074068-0.02193384619140.0543478567638-0.07969492888560.0982120160252-0.00431301836215-0.01501725498640.112600045622-0.008175868884060.0934253059367-12.8770000883-14.15056538499.73068771383
25.58535405352-0.9293410807061.330501350274.56082238727-0.2043123001693.60349365631-0.06111767934930.128691984319-0.256060906016-0.08100061829660.07760364897890.2279253145780.0181529761034-0.113926847411-0.02942930183650.0959595454958-0.0175116443308-0.00895154664280.111125046186-0.01338615157130.0747996112833-20.8634039317-18.70469469876.41453236028
32.17635502379-1.32328399929-0.4739495123781.217092146210.1233264207660.1702618880920.1146727168670.5891080864820.0695507297092-0.156033418518-0.0530533929820.1353692752180.16585903632-0.0355625252692-0.06457992898880.1898959692340.00803889639297-0.01617811199470.225425974020.01262475424120.116155164725-18.9090597515-11.20554525711.13322096688
44.71720591805-2.305922091695.059716810212.84167994027-2.627650753125.44086352951-0.00254671199180.0769512106284-0.06629281079590.100008659204-0.0367953648532-0.003674145938940.007861346710190.1527892168010.06075131875220.1226194140420.0254417033970.01497677565960.143263193493-0.001872842007160.132360026334-2.76377475147-20.35887764812.0806302822
53.99918369451-2.950934991943.506426115124.28668585721-3.369492881936.956149184350.01883122545720.1887578090340.0436854311298-0.127758999072-0.0882939289074-0.196311033950.07635407741750.1971145438640.01795587694150.09504227127310.0001115781022950.009794702113890.118214405044-0.001089631126810.116609859171-3.15813922085-9.790753384156.59310026503
61.931936090610.2808631493720.04184131669062.37265691206-0.8334555229372.86752456346-0.0123421623788-0.07491444492120.03257926425960.0318789068520.0453502801185-0.142695202248-0.1078173473960.132683057699-0.009247264512230.09615894663920.007084826059710.0103736836920.0995347843435-0.01296189853090.0845529397568-8.48840192624-8.2363825103614.5714139794
72.229094311220.628838483821-0.7172945792071.01326271959-0.3442709510851.005719120820.0243023165212-0.08519836244330.1187891172510.04904796096070.0116994127012-0.0738839328611-0.06923563476840.0456480893726-0.05496262621380.115833290373-0.0007814266267930.0002801385907820.099516351815-0.01940565329460.0930836805559-10.3048791652-6.8659596984116.4780605453
84.17421690832-0.394981454078-0.6489090071574.99714348705-0.3172750397682.69484659459-0.0419613834579-0.09842582930050.5073177381870.09071607260240.0772022169340.138750337778-0.3878199855220.0818730937712-0.1072937401280.148020365381-0.0189393728298-0.002841148883880.137912989036-0.03532898951570.185029699368-10.20408762211.2472991357420.0830069869
91.06842777299-0.1831687908670.06737723455992.74014980393-0.2514902065871.468541979150.032012332312-0.135564391583-0.08594062529770.152022438173-0.02995193383670.09621260306470.107221757382-0.05715605758060.0247785354230.135270059366-0.005582750684770.01761384556690.1344425688790.001667362280780.0955861042775-18.6224299268-14.897543995825.5994237823
102.249885721831.122633266280.2082272559147.210165849560.3557316406381.152275024480.0648191648929-0.1066042862460.06408768589310.17764890162-0.1063322265980.2109076738830.0509503718332-0.07070212411810.01215747535750.0963813580471-0.00660677413802-0.001968819057040.135521221074-0.004362828154320.0956389619343-25.0516137043-14.783152133615.452663166
113.786215663062.183960958685.100964728553.691486205493.274751476238.21644435584-0.1044000565370.02083478833940.223965620948-0.003250397039770.1094125253550.0289325640611-0.4888710760530.128598508611-0.115767763830.1747462607170.0008073367231260.01064459712980.135231025613-0.03711880442830.158055273858-17.83243804291.7323250256921.6992671661
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 16 )4 - 161 - 13
22chain 'A' and (resid 17 through 30 )17 - 3014 - 27
33chain 'A' and (resid 31 through 39 )31 - 3928 - 36
44chain 'A' and (resid 40 through 48 )40 - 4837 - 45
55chain 'A' and (resid 49 through 67 )49 - 6746 - 64
66chain 'A' and (resid 68 through 90 )68 - 9065 - 87
77chain 'A' and (resid 91 through 109 )91 - 10988 - 106
88chain 'A' and (resid 110 through 124 )110 - 124107 - 121
99chain 'A' and (resid 125 through 158 )125 - 158122 - 155
1010chain 'A' and (resid 159 through 174 )159 - 174156 - 171
1111chain 'A' and (resid 175 through 184 )175 - 184172 - 181

+
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