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- PDB-2pyq: Crystal structure of a duf2853 member protein (jann_4075) from ja... -

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Basic information

Entry
Database: PDB / ID: 2pyq
TitleCrystal structure of a duf2853 member protein (jann_4075) from jannaschia sp. ccs1 at 1.500 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyJann4075-like / Protein of unknown function DUF2853 / Jann4075-like superfamily / Protein of unknown function (DUF2853) / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesJannaschia sp. CCS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (YP_512017.1) from Jannaschia sp. CCS1 at 1.500 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,0886
Polymers51,6994
Non-polymers3882
Water5,477304
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,9251
Polymers12,9251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,9251
Polymers12,9251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,9251
Polymers12,9251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3133
Polymers12,9251
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.920, 98.710, 58.560
Angle α, β, γ (deg.)90.000, 90.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 12924.854 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia sp. CCS1 (bacteria) / Gene: YP_512017.1, Jann_4075 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q28JX0
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NANODROP, 30.0% PEG 6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97910, 0.97886
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 8, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97911
30.978861
ReflectionResolution: 1.5→28.689 Å / Num. obs: 59568 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.524 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 7.77
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.550.4681.918894981388.7
1.55-1.620.3692.5265871310997.8
1.62-1.690.2883.1224651110798.1
1.69-1.780.2323.8240131184998.6
1.78-1.890.1724.9234121159398.9
1.89-2.040.1176.9244101212599.1
2.04-2.240.0789.7231101147899
2.24-2.560.05812.3236131172498.9
2.56-3.230.04714.5237321184598.4
3.230.03517.8225811145895.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PHENIXrefinement
SHELXphasing
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→28.689 Å / FOM work R set: 0.75 / Stereochemistry target values: twin_lsq_f
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. PEG 200 MOLECULES (PG4) ARE MODELED. 4. THE DATA ARE TWINNED WITH THE TWIN LAW -H,-K,L. THE REFINED TWIN FRACTION WAS 0.227. 5. DUE TO 4-FOLD NCS AND TWINNING, REFLECTIONS FOR R-FREE SET WERE SELECTED IN THIN SHELLS. 6. WHEN REFINING TLS, THE OUTPUT PDB FILE ALWAYS HAS THE ANISOU RECORDS FOR THE ATOMS INVOLVED IN TLS GROUPS. THE ANISOTROPIC B-FACTOR IN ANISOU RECORDS IS THE TOTAL B-FACTOR (B_TLS + B_INDIVIDUAL). THE ISOTROPIC EQUIVALENT B-FACTOR IN ATOM RECORDS IS THE MEAN OF THE TRACE OF THE ANISOU MATRIX DIVIDED BY 10000 AND MULTIPLIED BY 8*PI^2 AND REPRESENTS THE ISOTROPIC EQUIVALENT OF THE TOTAL B-FACTOR (B_TLS + B_INDIVIDUAL). TO OBTAIN THE INDIVIDUAL B-FACTORS, ONE NEEDS TO COMPUTE THE TLS COMPONENT (B_TLS) USING THE TLS RECORDS IN THE PDB FILE HEADER AND THEN SUBTRACT IT FROM THE TOTAL B-FACTORS (ON THE ANISOU RECORDS).
RfactorNum. reflection% reflection
Rfree0.195 6264 5.4 %
Rwork0.176 --
obs0.176 59537 97.7 %
Solvent computationBsol: 51.298 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 103.1 Å2 / Biso mean: 27.35 Å2 / Biso min: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å2-0 Å21.278 Å2
2---3.605 Å2-0 Å2
3---1.315 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3421 0 14 304 3739
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_deg1.1251
X-RAY DIFFRACTIONf_bond_d0.0131
X-RAY DIFFRACTIONfHIRAL0.0781
X-RAY DIFFRACTIONf_dihedral_angle_d9.3881
X-RAY DIFFRACTIONfLANE0.0051
X-RAY DIFFRACTIONfonbonded4.071
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)
11.43260.28-0.35881.9777-0.53411.36670.0512-0.0231-0.19210.2227-0.0419-0.05910.12370.0352-00.28640.0163-0.00710.2042-0.02280.19754.844931.58130.9323
21.5328-0.38660.25471.879-0.17131.43060.03350.01560.1434-0.2359-0.0035-0.0133-0.09780.023900.2359-0.014-0.0110.1878-0.02360.188621.38432.241956.7451
32.24140.1241-0.15962.29920.05261.41270.05030.0144-0.04470.0184-0.0823-0.05330.1549-0.0505-00.14280.0041-0.00060.17560.0090.1773-2.922457.69545.3009
41.79380.54030.32962.39250.19781.48420.04620.04840.07560.0117-0.0536-0.0129-0.09420.0356-00.14490.0115-0.0180.1779-0.00530.177118.818555.583574.4227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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