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- PDB-1xhn: The crystal structure of Cellular Repressor of E1A-stimulated Gen... -

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Basic information

Entry
Database: PDB / ID: 1xhn
TitleThe crystal structure of Cellular Repressor of E1A-stimulated Genes (CREG)
ComponentsCellular Repressor of E1A-stimulated Genes
KeywordsUNKNOWN FUNCTION / beta-barrel
Function / homology
Function and homology information


neutrophil degranulation / multicellular organism development / regulation of growth / transcription corepressor activity / azurophil granule lumen / Neutrophil degranulation / regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Cellular repressor of E1A-stimulated genes (CREG) / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsSacher, M. / Lunin, V.V. / Cygler, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: The crystal structure of CREG, a secreted glycoprotein involved in cellular growth and differentiation
Authors: Sacher, M. / Di Bacco, A. / Lunin, V.V. / Ye, Z. / Wagner, J. / Gill, G. / Cygler, M.
History
DepositionSep 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellular Repressor of E1A-stimulated Genes
B: Cellular Repressor of E1A-stimulated Genes
C: Cellular Repressor of E1A-stimulated Genes
D: Cellular Repressor of E1A-stimulated Genes


Theoretical massNumber of molelcules
Total (without water)83,0274
Polymers83,0274
Non-polymers00
Water16,069892
1
A: Cellular Repressor of E1A-stimulated Genes
B: Cellular Repressor of E1A-stimulated Genes


Theoretical massNumber of molelcules
Total (without water)41,5132
Polymers41,5132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-21 kcal/mol
Surface area14680 Å2
MethodPISA
2
C: Cellular Repressor of E1A-stimulated Genes
D: Cellular Repressor of E1A-stimulated Genes


Theoretical massNumber of molelcules
Total (without water)41,5132
Polymers41,5132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-22 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.130, 121.260, 55.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Cellular Repressor of E1A-stimulated Genes / CREG


Mass: 20756.713 Da / Num. of mol.: 4 / Fragment: residues 13-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O75629
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 44.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Na acetate, PEG4000, ethylene glycole, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979502, 0.980005, 0.972318
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795021
20.9800051
30.9723181
ReflectionResolution: 1.95→50 Å / Num. all: 51850 / Num. obs: 51850 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.95→2.02 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→19.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.698 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21314 1065 2.1 %RANDOM
Rwork0.16192 ---
all0.16299 50783 --
obs0.16299 50783 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---1.26 Å20 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 0 892 6402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0215688
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9377786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865685
X-RAY DIFFRACTIONr_chiral_restr0.1170.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024334
X-RAY DIFFRACTIONr_nbd_refined0.2170.22903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2700
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.244
X-RAY DIFFRACTIONr_mcbond_it0.9971.53473
X-RAY DIFFRACTIONr_mcangle_it1.70925705
X-RAY DIFFRACTIONr_scbond_it2.88732215
X-RAY DIFFRACTIONr_scangle_it4.2334.52081
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.201 69
Rwork0.167 3068

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