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- PDB-3t43: Crystal Structure of HIV Epitope-Scaffold 4E10_1XIZA_S0_006_C -

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Basic information

Entry
Database: PDB / ID: 3t43
TitleCrystal Structure of HIV Epitope-Scaffold 4E10_1XIZA_S0_006_C
ComponentsHIV Epitope-Scaffold 4E10_1XIZA_S0_006_C
KeywordsTRANSFERASE / Putative phosphotransferase system
Function / homologyMannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesartificial gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHolmes, M.A. / Strong, R.K.
CitationJournal: Protein Sci. / Year: 2011
Title: High-resolution structure prediction of a circular permutation loop.
Authors: Correia, B.E. / Holmes, M.A. / Huang, P.S. / Strong, R.K. / Schief, W.R.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV Epitope-Scaffold 4E10_1XIZA_S0_006_C
B: HIV Epitope-Scaffold 4E10_1XIZA_S0_006_C


Theoretical massNumber of molelcules
Total (without water)36,5072
Polymers36,5072
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-13 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.060, 65.270, 73.100
Angle α, β, γ (deg.)90.000, 99.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIV Epitope-Scaffold 4E10_1XIZA_S0_006_C


Mass: 18253.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 4000, 20% Isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 17, 2007
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→30.31 Å / Num. obs: 24452 / % possible obs: 99.7 % / Redundancy: 3.04 % / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.052 / Χ2: 0.96 / Net I/σ(I): 12.5 / Num. measured all: 74779 / Scaling rejects: 561
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.95-2.021.840.2732450124311.071699.6
2.02-2.12.140.222.8520224151.072399.5
2.1-2.22.430.183.5595424291.014999.8
2.2-2.312.70.1415661224341.044899.5
2.31-2.463.10.126.47642244714699.8
2.46-2.653.570.1077.38728243414999.9
2.65-2.913.620.07710.4885324350.9337100
2.91-3.333.640.05216.1902524680.914499.9
3.33-4.23.660.03524.5903224470.887299.8
4.2-30.313.60.02931.7923025120.9217799.4

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.7Ddata reduction
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LF6

3lf6


Resolution: 1.95→30.31 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.918 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 1249 5.1 %RANDOM
Rwork0.204 ---
obs0.2063 23184 99.66 %-
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 max: 70.68 Å2 / Biso mean: 44.3047 Å2 / Biso min: 26.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.02 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 0 194 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222496
X-RAY DIFFRACTIONr_bond_other_d0.0010.021615
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9453423
X-RAY DIFFRACTIONr_angle_other_deg0.77533963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7115321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99424.286112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0615391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3991514
X-RAY DIFFRACTIONr_chiral_restr0.0620.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022800
X-RAY DIFFRACTIONr_gen_planes_other00.02489
X-RAY DIFFRACTIONr_nbd_refined0.2040.3509
X-RAY DIFFRACTIONr_nbd_other0.2010.31784
X-RAY DIFFRACTIONr_nbtor_refined0.1810.51232
X-RAY DIFFRACTIONr_nbtor_other0.0880.51217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.5261
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0870.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3770.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.519
X-RAY DIFFRACTIONr_mcbond_it0.93621605
X-RAY DIFFRACTIONr_mcbond_other0.1962621
X-RAY DIFFRACTIONr_mcangle_it1.53532566
X-RAY DIFFRACTIONr_scbond_it1.98741001
X-RAY DIFFRACTIONr_scangle_it2.946849
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 95 -
Rwork0.244 1720 -
all-1815 -
obs--99.51 %

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