[English] 日本語
Yorodumi
- PDB-7mjb: Crystal Structure of Nanoluc Luciferase Mutant R164Q -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mjb
TitleCrystal Structure of Nanoluc Luciferase Mutant R164Q
ComponentsNanoluc Luciferase
KeywordsOXIDOREDUCTASE / BIOLUMINESCENT PROTEIN / NANOLUC LUCIFERASE
Function / homologyDECANOIC ACID / NITRATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShabalin, I.G. / Reza, M.S. / Ai, H. / Minor, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Nanoluc Luciferase Mutant R164Q
Authors: Shabalin, I.G. / Reza, M.S. / Ai, H. / Minor, W.
History
DepositionApr 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Nanoluc Luciferase
B: Nanoluc Luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6859
Polymers41,0132
Non-polymers6727
Water4,918273
1
A: Nanoluc Luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9446
Polymers20,5061
Non-polymers4385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nanoluc Luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7413
Polymers20,5061
Non-polymers2342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.180, 62.045, 97.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 171 / Label seq-ID: 14 - 184

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Nanoluc Luciferase


Mass: 20506.324 Da / Num. of mol.: 2 / Mutation: R164Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oplophorus gracilirostris (crustacean) / Production host: Escherichia coli (E. coli) / References: Oplophorus-luciferin 2-monooxygenase

-
Non-polymers , 5 types, 280 molecules

#2: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 0.2 ul of 9 mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP. Precipitant: 0.2uL 0.2M Na nitrate, 20%w/v PEG 3350 (MCSG Suite 2 #34). Cryo- ...Details: Protein: 0.2 ul of 9 mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP. Precipitant: 0.2uL 0.2M Na nitrate, 20%w/v PEG 3350 (MCSG Suite 2 #34). Cryo-protection: air-drying (slow dehydration)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2020
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 40852 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.017 / Rrim(I) all: 0.042 / Χ2: 0.908 / Net I/av σ(I): 41.9 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allRsym valueΧ2% possible all
1.7-1.735.91.1141.720160.6820.9010.4961.2211.1140.961100
1.73-1.765.90.9620170.740.4281.0520.941100
1.76-1.795.90.74619880.7960.3350.820.96899.8
1.79-1.835.80.58820430.8790.2650.6460.986100
1.83-1.875.80.41719940.9280.1890.4580.96699.9
1.87-1.915.70.30520190.9630.1390.3360.98100
1.91-1.965.50.22320280.9730.1030.2461.01699.9
1.96-2.0250.17919940.9770.0880.21.04699.9
2.02-2.0760.16120480.9870.0720.1770.949100
2.07-2.145.90.12520170.990.0560.1370.937100
2.14-2.225.90.09220500.9940.0410.1010.922100
2.22-2.315.90.07520120.9960.0340.0830.87999.9
2.31-2.415.80.06520400.9960.0290.0710.817100
2.41-2.545.30.05120100.9970.0240.0570.77299.6
2.54-2.75.70.04320600.9980.020.0470.794100
2.7-2.916.10.03520400.9980.0150.0390.78799.9
2.91-3.25.90.0320800.9980.0130.0330.809100
3.2-3.665.40.02720770.9980.0130.030.8499.9
3.66-4.615.70.02621000.9990.0120.0290.93599.7
4.61-505.30.02622190.9980.0120.0290.87199.3

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IBO

5ibo


Resolution: 1.7→39.51 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.564 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 1837 4.9 %RANDOM
Rwork0.1726 ---
obs0.1739 35957 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.59 Å2 / Biso mean: 30.486 Å2 / Biso min: 1.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2---0.32 Å20 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 1.7→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 43 273 2944
Biso mean--30.72 33.38 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132762
X-RAY DIFFRACTIONr_bond_other_d0.0050.0172661
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.6313758
X-RAY DIFFRACTIONr_angle_other_deg1.361.5766109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0425350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09423.308133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39915449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2351512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
Refine LS restraints NCS

Ens-ID: 1 / Number: 4963 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 67 -
Rwork0.241 1333 -
all-1400 -
obs--47.17 %
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)
12.00091.10640.12123.55630.76942.9847-0.28630.11580.1859-0.46190.1327-0.0468-0.2486-0.04190.15350.0843-0.005-0.02710.0838-0.02490.05370.57814.41834.636
25.90571.5651-0.74992.15990.37721.9691-0.24460.05820.0399-0.20250.1873-0.0777-0.03980.24020.05740.0264-0.0045-0.00150.0935-0.02660.02888.1359.60838.12
32.9882-0.08720.03528.73462.24513.4105-0.0682-0.1242-0.0226-0.20480.256-0.9638-0.01460.5258-0.18790.022-0.02060.04110.1532-0.0430.127118.262.54233.401
44.41410.3897-0.43641.57730.37951.2715-0.1276-0.14450.24560.08620.1284-0.086-0.09250.0991-0.00070.026-0.0003-0.0150.1635-0.07340.06885.39216.62647.891
52.89533.10911.3017.00212.19333.07-0.1506-0.03590.2443-0.49420.06280.1576-0.2769-0.02340.08780.0524-0.0071-0.01060.0837-0.00470.0629-0.51416.52434.045
64.51621.45990.16015.36732.58097.6775-0.08880.06760.1903-0.6147-0.035-0.3198-0.27170.32570.12380.3457-0.00620.03830.10160.04650.066114.4524.16613.502
73.7261-1.4494-2.5157.56033.06188.76080.16870.06980.2746-0.8222-0.0152-0.0635-0.359-0.045-0.15340.4556-0.02680.0140.17820.01260.05326.767.3259.447
88.43510.3571-1.96155.54440.94645.92180.05680.20711.2231-0.62670.02820.2531-0.77450.0537-0.08510.3887-0.0115-0.06430.16470.04430.1941-2.98918.32715.41
95.5586-3.6173-6.41555.96657.017910.45350.30740.03050.3343-1.10810.1858-0.419-0.60310.173-0.49310.7757-0.03440.12850.23910.04360.093810.06210.5090.93
101.5690.5574-1.11875.6214-0.7566.1988-0.03590.00090.0391-1.0684-0.0743-0.7494-0.3640.65150.11030.5513-0.05880.17420.20650.01040.150417.6535.7238.965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 26
2X-RAY DIFFRACTION2A27 - 58
3X-RAY DIFFRACTION3A59 - 95
4X-RAY DIFFRACTION4A96 - 140
5X-RAY DIFFRACTION5A141 - 171
6X-RAY DIFFRACTION6B1 - 26
7X-RAY DIFFRACTION7B27 - 58
8X-RAY DIFFRACTION8B59 - 91
9X-RAY DIFFRACTION9B92 - 116
10X-RAY DIFFRACTION10B117 - 171

+
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://pdbjlvh1.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