[English] 日本語
Yorodumi
- PDB-3lo3: The crystal structure of a conserved functionally unknown protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lo3
TitleThe crystal structure of a conserved functionally unknown protein from Colwellia psychrerythraea 34H.
Componentsuncharacterized conserved protein
Keywordsstructure genomics / unknown function / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyDomain of unknown function DUF1330 / Domain of unknown function (DUF1330) / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / DUF1330 domain-containing protein
Function and homology information
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.383 Å
AuthorsTan, K. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved functionally unknown protein from Colwellia psychrerythraea 34H.
Authors: Tan, K. / Li, H. / Bearden, J. / Joachimiak, A.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Sep 5, 2012Group: Derived calculations

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized conserved protein
B: uncharacterized conserved protein
C: uncharacterized conserved protein
D: uncharacterized conserved protein
E: uncharacterized conserved protein
F: uncharacterized conserved protein
G: uncharacterized conserved protein
H: uncharacterized conserved protein
I: uncharacterized conserved protein
J: uncharacterized conserved protein
K: uncharacterized conserved protein
L: uncharacterized conserved protein
M: uncharacterized conserved protein
N: uncharacterized conserved protein
O: uncharacterized conserved protein
P: uncharacterized conserved protein
Q: uncharacterized conserved protein
R: uncharacterized conserved protein
S: uncharacterized conserved protein
T: uncharacterized conserved protein
U: uncharacterized conserved protein
V: uncharacterized conserved protein
W: uncharacterized conserved protein
X: uncharacterized conserved protein
Y: uncharacterized conserved protein
Z: uncharacterized conserved protein
a: uncharacterized conserved protein
b: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,04732
Polymers296,67928
Non-polymers3684
Water8,269459
1
A: uncharacterized conserved protein
B: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-10 kcal/mol
Surface area9400 Å2
MethodPISA
2
C: uncharacterized conserved protein
D: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2833
Polymers21,1912
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-11 kcal/mol
Surface area9470 Å2
MethodPISA
3
E: uncharacterized conserved protein
F: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-10 kcal/mol
Surface area9800 Å2
MethodPISA
4
G: uncharacterized conserved protein
H: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-13 kcal/mol
Surface area9590 Å2
MethodPISA
5
I: uncharacterized conserved protein
J: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-11 kcal/mol
Surface area9570 Å2
MethodPISA
6
K: uncharacterized conserved protein
L: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-7 kcal/mol
Surface area9400 Å2
MethodPISA
7
M: uncharacterized conserved protein
N: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-11 kcal/mol
Surface area9610 Å2
MethodPISA
8
Q: uncharacterized conserved protein
R: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-12 kcal/mol
Surface area9660 Å2
MethodPISA
9
S: uncharacterized conserved protein
T: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2833
Polymers21,1912
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-10 kcal/mol
Surface area9520 Å2
MethodPISA
10
U: uncharacterized conserved protein
V: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-11 kcal/mol
Surface area9550 Å2
MethodPISA
11
W: uncharacterized conserved protein
X: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-11 kcal/mol
Surface area9700 Å2
MethodPISA
12
Y: uncharacterized conserved protein
Z: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-14 kcal/mol
Surface area9730 Å2
MethodPISA
13
a: uncharacterized conserved protein
b: uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)21,1912
Polymers21,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-12 kcal/mol
Surface area9590 Å2
MethodPISA
14
O: uncharacterized conserved protein
P: uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3764
Polymers21,1912
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.684, 109.503, 126.509
Angle α, β, γ (deg.)66.02, 80.80, 79.42
Int Tables number1
Space group name H-MP1
DetailsExperimentally unknown. The chains A and B, C and D, E and F, G and H, I and J, K and L, M and N, O and P, Q and R, S and T, U and V, W and X, Y and Z, a and b may form dimers, respectively.

-
Components

#1: Protein ...
uncharacterized conserved protein


Mass: 10595.670 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / Gene: CPS_1673 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q484V4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1M CHES, 20% w/v PEG8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912, 0.97937
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979121
20.979371
ReflectionResolution: 2.383→115 Å / Num. all: 103654 / Num. obs: 103654 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.9
Reflection shellResolution: 2.39→2.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5155 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.383→43.034 Å / SU ML: 0.44 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2766 4808 5 %randon
Rwork0.1902 ---
all0.1946 96204 --
obs0.1946 96204 90.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.972 Å2 / ksol: 0.33 e/Å3
Refinement stepCycle: LAST / Resolution: 2.383→43.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20860 0 24 459 21343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821309
X-RAY DIFFRACTIONf_angle_d1.20928789
X-RAY DIFFRACTIONf_dihedral_angle_d20.3237603
X-RAY DIFFRACTIONf_chiral_restr0.0853109
X-RAY DIFFRACTIONf_plane_restr0.0043726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3832-2.46840.35943920.24287328X-RAY DIFFRACTION72
2.4684-2.56720.36264480.24998273X-RAY DIFFRACTION82
2.5672-2.6840.34214360.22458551X-RAY DIFFRACTION84
2.684-2.82550.32464750.21758947X-RAY DIFFRACTION88
2.8255-3.00250.34724560.22539113X-RAY DIFFRACTION90
3.0025-3.23430.29384790.20669566X-RAY DIFFRACTION94
3.2343-3.55960.2845240.18549772X-RAY DIFFRACTION97
3.5596-4.07440.25345010.16669952X-RAY DIFFRACTION98
4.0744-5.13190.21885410.14229963X-RAY DIFFRACTION98
5.1319-43.0410.22985560.15979931X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.00290.615-0.36120.3763-0.55561.43890.0102-0.25650.0382-0.2281-0.17350.03960.15160.1070.12770.14820.02420.00590.0689-0.0270.0999-7.759251.7266-33.7863
20.90570.3674-0.28361.4389-0.48371.3319-0.06170.02970.0775-0.35130.170.03980.197-0.0162-0.06070.17990.03060.05370.0652-0.03840.0452
31.50690.08710.10871.38320.66650.8712-0.00690.16750.01720.1434-0.10970.08530.0004-0.08320.09980.0733-0.02770.01760.091-0.01020.0738
40.93390.17-0.01670.47370.54142.0430.00370.12460.1619-0.0088-0.1062-0.07390.13370.30160.09460.0846-0.00910.07250.14510.04290.1882
51.8740.2555-0.36861.732-1.41342.52560.11380.02810.1478-0.36680.1064-0.02270.3965-0.4834-0.19570.1278-0.07960.01880.16810.03470.0392
61.0326-0.1019-0.2770.7835-0.66591.68780.1804-0.03910.168-0.08650.09050.0473-0.1724-0.2679-0.21410.16360.0390.11040.14980.03250.1307
7-0.00470.2216-0.20750.6313-0.85471.3841-0.1482-0.0054-0.1519-0.1966-0.1097-0.0790.44680.09450.22320.40070.02150.15820.03920.00660.1443
82.11080.1423-1.43611.787-0.78131.7087-0.09010.66120.0977-0.53860.31520.07830.1896-0.7169-0.20830.51270.03220.11660.28230.04350.0549
90.63720.153-0.14441.10660.28821.38180.0515-0.10710.1054-0.0133-0.242-0.10770.250.19760.14980.1738-0.01390.0750.13260.0530.1464
100.4650.51840.2491.2901-1.42041.8744-0.1206-0.0803-0.0929-0.5745-0.2666-0.27230.75190.07330.37660.47050.10060.27860.14810.03470.2305
110.71790.1835-0.77771.8137-0.59271.6179-0.00080.0751-0.0945-0.31620.0773-0.10980.0636-0.1928-0.08290.158-0.01140.04020.1273-0.00110.129
120.72630.6389-0.97490.828-0.59332.0752-0.0342-0.1186-0.1156-0.0271-0.08190.0302-0.10.3640.0410.2420.00480.14440.1060.05510.1455
131.94890.9681-1.08510.7363-0.57412.0161-0.06460.2124-0.01370.21030.0999-0.08010.3551-0.28770.00460.2328-0.0750.04420.0772-0.00740.1
142.02160.6895-1.45290.1915-0.90262.04210.39660.53920.37540.18570.03890.1582-0.3782-0.516-0.36740.17870.05750.11050.27950.12380.1861
151.0569-1.07370.80450.98230.15860.9136-0.4005-0.14760.03090.39340.1890.0422-0.3104-0.07270.18810.46490.1-0.1350.1427-0.03340.1554
160.451-0.35820.68991.4495-0.03211.5423-0.23750.11360.17870.2169-0.1352-0.1676-0.23440.23740.30350.50120.0787-0.13480.16950.02830.1687
170.67210.22010.37320.489-0.37231.6352-0.05840.0257-0.00940.26020.0822-0.1371-0.0264-0.0943-0.00550.14490.0151-0.04970.053-0.03640.1311
180.7278-0.6110.48851.4506-0.7682.6452-0.1839-0.17970.09680.27160.166-0.2779-0.9604-0.57880.07070.4060.1591-0.07070.1058-0.030.1166
190.428-0.23340.54773.154-1.1391.714-0.05560.02370.121-0.1392-0.214-0.212-0.0440.30680.23630.13430.0029-0.04230.18710.03990.1616
201.0114-0.21020.83880.8025-0.42940.9504-0.0723-0.07080.0146-0.15440.09640.14490.0305-0.1051-0.00620.18660.0442-0.12840.0855-0.03280.122
212.495-1.68081.7752.1001-2.1082.1032-0.21370.06280.14020.66620.0978-0.2187-0.3975-0.01580.18330.2641-0.0378-0.11840.12390.02010.1401
221.8756-0.84530.81681.7449-1.6191.23210.28180.49910.0905-0.0931-0.4728-0.23830.12850.40760.19780.1340.0595-0.07920.26740.05610.1521
232.103-0.11720.20830.5897-0.75411.02140.0018-0.383-0.36690.04120.0134-0.0072-0.1112-0.248-0.0290.12090.0435-0.03080.15720.03540.1338
242.0009-0.52550.12650.7666-0.19411.7758-0.1288-0.09360.0298-0.10.01520.0243-0.28370.04150.13160.11980.0076-0.06920.059-0.01680.1277
250.51430.03550.8551.91380.08251.4105-0.1490.14270.2412-0.03140.0272-0.23040.08810.14120.12980.0019-0.0096-0.04530.13210.03420.1635
260.52350.5463-0.10650.7796-0.18290.68680.00330.10590.0014-0.01190.03150.1002-0.1388-0.165-0.05340.08940.0564-0.10440.19830.00290.1921
272.0573-0.38080.65160.8684-1.1242.69360.02250.27850.03940.2164-0.5555-0.2972-0.6410.67850.49440.2855-0.1187-0.19190.32270.18810.274
282.4371-0.4441-0.05122.5101-0.80141.75750.15020.0058-0.1501-0.4345-0.4962-0.07150.10590.4350.29180.15220.1288-0.03880.16970.01540.0774
Refinement TLS groupSelection details: chain b

+
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