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- PDB-2i5t: Crystal Structure of hypothetical protein LOC79017 from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 2i5t
TitleCrystal Structure of hypothetical protein LOC79017 from Homo sapiens
ComponentsProtein C7orf24
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


gamma-glutamylcyclotransferase / gamma-glutamylcyclotransferase activity / Glutathione synthesis and recycling / release of cytochrome c from mitochondria / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Gamma-glutamylcyclotransferase / AIG2-like family / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-glutamylcyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsBae, E. / Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of Homo sapiens protein LOC79017.
Authors: Bae, E. / Bingman, C.A. / Aceti, D.J. / Phillips Jr., G.N.
History
DepositionAug 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein C7orf24
B: Protein C7orf24


Theoretical massNumber of molelcules
Total (without water)42,3462
Polymers42,3462
Non-polymers00
Water2,540141
1
A: Protein C7orf24


Theoretical massNumber of molelcules
Total (without water)21,1731
Polymers21,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein C7orf24


Theoretical massNumber of molelcules
Total (without water)21,1731
Polymers21,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.052, 100.138, 102.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThere are 2 biological units in the asymmetric unit (chains A & B)

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Components

#1: Protein Protein C7orf24


Mass: 21173.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C7orf24 / Plasmid: PVP 30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) pRARE2 / References: UniProt: O75223
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.2 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M BISTRIS PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (28% PEG 2K, 0.20 M ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M BISTRIS PH 7.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (28% PEG 2K, 0.20 M POTASSIUM GLUTAMATE, 0.1 M MES/ACETATE PH 5.5) CRYOPROTECTED WITH 10% ETHYLENE GLYCOL IN WELL SOLUTION, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATER / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.01→45.621 Å / Num. obs: 24297 / % possible obs: 97.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 12.185
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 4.096 / % possible all: 83.2

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Phasing

PhasingMethod: SAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 2.01 Å / Lowest resolution: 44.99 Å / Power centric: 0

IDR cullis acentricPower acentricReflection acentricReflection centric
ISO_100210103203
ANO_10.7691.243204870
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_18.83-44.9900189154
ISO_16.3-8.8300404167
ISO_15.16-6.300531163
ISO_14.48-5.1600650163
ISO_14.01-4.4800741165
ISO_13.66-4.0100834169
ISO_13.39-3.6600900170
ISO_13.17-3.3900978159
ISO_12.99-3.17001056166
ISO_12.84-2.99001117173
ISO_12.71-2.84001151153
ISO_12.59-2.71001256175
ISO_12.49-2.59001273168
ISO_12.4-2.49001355167
ISO_12.32-2.4001387166
ISO_12.25-2.32001442161
ISO_12.18-2.25001436148
ISO_12.12-2.18001500160
ISO_12.06-2.12001449135
ISO_12.01-2.06001361121
ANO_18.83-44.990.3054.381890
ANO_16.3-8.830.2844.6864040
ANO_15.16-6.30.3114.185310
ANO_14.48-5.160.423.1896500
ANO_14.01-4.480.4972.6177410
ANO_13.66-4.010.572.4058340
ANO_13.39-3.660.5832.2089000
ANO_13.17-3.390.6171.979780
ANO_12.99-3.170.6311.77710560
ANO_12.84-2.990.6821.4811170
ANO_12.71-2.840.7521.32111510
ANO_12.59-2.710.8021.13412560
ANO_12.49-2.590.8430.94212730
ANO_12.4-2.490.8870.80513510
ANO_12.32-2.40.9070.68113760
ANO_12.25-2.320.9350.65214140
ANO_12.18-2.250.9460.55713770
ANO_12.12-2.180.9580.50214120
ANO_12.06-2.120.9640.48512910
ANO_12.01-2.060.9690.43911860
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-0.879-76.64-18.638SE25.331.47
214.226-79.645-33.733SE24.851.51
33.264-96.217-19.476SE35.751.52
418.852-82.323-53.198SE30.691.35
55.52-89.058-2.037SE27.651.11
6-3.421-101.8848.49SE22.511.01
710.172-89.432-6.172SE38.340.66
8-8.501-105.6287.469SE58.510.98
9-27.246-47.581-7.468SE14.840.26
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 24211
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.77-10071.20.691502
6.09-7.7767.80.842504
5.28-6.0967.10.896509
4.75-5.2863.20.928530
4.36-4.7559.80.92564
4.04-4.3659.50.932641
3.79-4.0463.40.916656
3.58-3.7964.90.916705
3.4-3.5862.10.901743
3.25-3.467.60.902769
3.11-3.25660.889805
2.99-3.1167.80.896836
2.89-2.9965.70.893867
2.79-2.8967.90.9895
2.7-2.7970.80.897893
2.62-2.773.30.886982
2.55-2.6272.20.879981
2.48-2.5572.30.893988
2.42-2.4875.40.8951037
2.36-2.4274.10.8991035
2.31-2.3674.60.8991052
2.26-2.3180.50.8771112
2.21-2.2680.60.9011084
2.17-2.2183.50.8941104
2.13-2.1780.30.9071120
2.09-2.1382.70.8681106
2.05-2.0982.10.8231077
2.01-2.0583.10.7421114

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.01→45.62 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.02 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL DIFFERENCE ELECTRON DENSITY MAP SHOWS EXTENSIVE POSITIVE ELECTRON DENSITY WITHIN THE REGION SURROUNDED BY RESIDUES TYR 19, TYR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FINAL DIFFERENCE ELECTRON DENSITY MAP SHOWS EXTENSIVE POSITIVE ELECTRON DENSITY WITHIN THE REGION SURROUNDED BY RESIDUES TYR 19, TYR 22, GLY 23, SER 24, ASN 25, GLU 98, TYR 105 AND TYR 139. ATTEMPTS TO MODEL THIS DENSITY WITH CRYSTALLIZATION SOLUTION COMPONENTS WERE UNSUCCESSFUL. THE DEPOSITED STRUCTURE FACTOR FILE MAY BE USED TO EXAMINE THIS DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1233 5.092 %RANDOM
Rwork0.183 ---
obs0.186 24213 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 23.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.436 Å20 Å20 Å2
2--1.092 Å20 Å2
3----0.657 Å2
Refinement stepCycle: LAST / Resolution: 2.01→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 0 141 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222804
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9593792
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92725.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67615513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.502158
X-RAY DIFFRACTIONr_chiral_restr0.1140.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022138
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21243
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21919
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.71121783
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.01242777
X-RAY DIFFRACTIONr_scbond_it5.53561197
X-RAY DIFFRACTIONr_scangle_it7.90981015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 67 -
Rwork0.203 1416 -
obs--82.11 %

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