[English] 日本語
Yorodumi
- PDB-4nrd: Crystal structure of a putative GDSL-like lipase (BACOVA_04955) f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nrd
TitleCrystal structure of a putative GDSL-like lipase (BACOVA_04955) from Bacteroides ovatus ATCC 8483 at 2.10 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Lipase_GDSL_lke protein / PF16255 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyPutative GDSL-like Lipase/Acylhydrolase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_04955) from Bacteroides ovatus ATCC 8483 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,6479
Polymers161,4616
Non-polymers1863
Water6,684371
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7924
Polymers80,7303
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-7 kcal/mol
Surface area24770 Å2
MethodPISA
2
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8555
Polymers80,7303
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-1 kcal/mol
Surface area24840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.941, 70.895, 76.618
Angle α, β, γ (deg.)88.780, 84.700, 60.130
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Uncharacterized protein


Mass: 26910.125 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_04955 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M4B4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY RESIDUES 21-228 OF THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.00M lithium chloride, 20.00% polyethylene glycol 6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97937
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.1→29.391 Å / Num. all: 61839 / Num. obs: 61839 / % possible obs: 82.2 % / Redundancy: 2.3 % / Rsym value: 0.102 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.152.30.4631.91078147440.46384.3
2.15-2.212.30.3652.21017944330.36582.3
2.21-2.282.30.3362.4909340100.33676.1
2.28-2.352.20.2962.6865438660.29675.4
2.35-2.422.30.2772.8982942680.27786.3
2.42-2.512.30.2293.3960941620.22986.4
2.51-2.62.30.1873.7877038640.18783.7
2.6-2.712.30.1724.2833236540.17281.3
2.71-2.832.30.1435691230570.14371.8
2.83-2.972.30.1175.9798934910.11785.2
2.97-3.132.30.0937.1773333310.09386.1
3.13-3.322.30.0848.1729331800.08486
3.32-3.552.30.0719.5652228620.07182.5
3.55-3.832.20.05911.8542824150.05976
3.83-4.22.30.05813619926680.05889.7
4.2-4.72.30.05813.4536123200.05886.7
4.7-5.422.20.05513400317880.05575.8
5.42-6.642.30.06311.9396117200.06387.4
6.64-9.392.30.05812.9304113160.05884.9
9.39-29.3912.30.06415.415846900.06482.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.391 Å / Cor.coef. Fo:Fc: 0.9478 / Cor.coef. Fo:Fc free: 0.9277 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM ...Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT USING LSSR (-AUTONCS) IN BUSTER. 7. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 3082 4.99 %RANDOM
Rwork0.1701 ---
obs0.1719 61819 82.22 %-
Displacement parametersBiso max: 129.61 Å2 / Biso mean: 39.8132 Å2 / Biso min: 3.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.5248 Å22.2362 Å20.7448 Å2
2--3.7015 Å20.4491 Å2
3----4.2263 Å2
Refine analyzeLuzzati coordinate error obs: 0.296 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10101 0 12 371 10484
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5523SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes277HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2980HARMONIC5
X-RAY DIFFRACTIONt_it20145HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1360SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact21218SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20145HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg36150HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion2.97
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2675 223 4.72 %
Rwork0.2041 4506 -
all0.2071 4729 -
obs--82.22 %
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)
12.51930.4880.2843.17220.01030.7354-0.00370.132-0.1651-0.09050.001-0.2467-0.00970.04360.0027-0.29860.00280.0269-0.2432-0.03270.30848.003-26.166141.1648
22.61680.5377-0.26483.4747-0.21810.78470.05690.02780.1766-0.0572-0.032-0.0158-0.0097-0.0518-0.0249-0.33360.0120.0097-0.2323-0.07860.335553.44328.611341.1804
32.8981-0.2675-0.01323.14070.00130.38740.02220.12120.0128-0.16590.01020.42560.0534-0.0005-0.0324-0.33070.01230.0527-0.2702-0.05310.365220.3463-4.073641.165
42.75020.1596-0.08382.65350.01570.4812-0.01440.09180.0136-0.1731-0.002-0.2266-0.0642-0.00180.0163-0.30540.02560.0124-0.2643-0.04930.329622.281612.12053.3649
53.89880.61470.04282.63460.19780.6293-0.09380.28840.2259-0.07030.10930.1308-0.0047-0.0513-0.0155-0.2966-0.01110.0191-0.2337-0.04460.3006-5.229534.50673.396
63.4076-0.46060.16122.57320.2540.68550.03690.236-0.2653-0.1079-0.04640.10540.03550.05860.0095-0.34-0.00810.048-0.2517-0.02880.3177-10.6241-0.28493.4957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|21-227 }
2X-RAY DIFFRACTION2{ B|21-226 }
3X-RAY DIFFRACTION3{ C|21-227 }
4X-RAY DIFFRACTION4{ D|21-227 }
5X-RAY DIFFRACTION5{ E|21-226 }
6X-RAY DIFFRACTION6{ F|21-227 }

+
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