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- PDB-3rpt: Crystal structure of the anti-HIV b12 scaffold protein -

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Basic information

Entry
Database: PDB / ID: 3rpt
TitleCrystal structure of the anti-HIV b12 scaffold protein
ComponentsEndoglucanase E-2
KeywordsHYDROLASE / scaffold protein anti-HIV
Function / homology
Function and homology information


cellulase / polysaccharide binding / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / 1, 4-beta cellobiohydrolase / Cellulose binding domain ...Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / 1, 4-beta cellobiohydrolase / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.303 Å
AuthorsChen, L. / Kwong, P.D.
CitationJournal: Science / Year: 2011
Title: Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.
Authors: Azoitei, M.L. / Correia, B.E. / Ban, Y.E. / Carrico, C. / Kalyuzhniy, O. / Chen, L. / Schroeter, A. / Huang, P.S. / McLellan, J.S. / Kwong, P.D. / Baker, D. / Strong, R.K. / Schief, W.R.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Endoglucanase E-2
A: Endoglucanase E-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7483
Polymers59,6522
Non-polymers961
Water6,431357
1
X: Endoglucanase E-2


Theoretical massNumber of molelcules
Total (without water)29,8261
Polymers29,8261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endoglucanase E-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9222
Polymers29,8261
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.867, 46.240, 62.282
Angle α, β, γ (deg.)78.57, 81.80, 61.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Endoglucanase E-2 / Cellulase E-2 / Cellulase E2 / Endo-1 / 4-beta-glucanase E-2


Mass: 29825.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: celB / Production host: Escherichia coli (E. coli) / References: UniProt: P26222, cellulase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SUBMITTED SEQUENCE IS DIFFERENT FROM THE REFERENCE SEQUENCE. REMARK 999 THE REFERENCE PROTEIN ...THE SUBMITTED SEQUENCE IS DIFFERENT FROM THE REFERENCE SEQUENCE. REMARK 999 THE REFERENCE PROTEIN WAS USED AS BACKBONE. A NEW SCAFFOLDING REMARK 999 PROTEIN WAS GENERATED BY INSERTING AND DELETING CERTAIN RESIDUES.

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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: 1.9 Å3/Da / Density % sol: 35.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M Li2SO4,0.1 M MgSO4, 0.1 M acetate pH 4.5, and 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2009
RadiationMonochromator: Si 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionLowest resolution: 50 Å / Num. all: 85025 / % possible obs: 79.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.29→1.31 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3 / % possible all: 76.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.303→26.207 Å / SU ML: 0.16 / σ(F): 0.04 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.202 4099 5.07 %random
Rwork0.1735 ---
obs0.175 80860 75.46 %-
all-65145 --
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.361 Å2 / ksol: 0.484 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.4878 Å21.5095 Å22.5509 Å2
2---3.3393 Å21.4012 Å2
3----6.1484 Å2
Refinement stepCycle: LAST / Resolution: 1.303→26.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 5 357 4136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113940
X-RAY DIFFRACTIONf_angle_d1.2515382
X-RAY DIFFRACTIONf_dihedral_angle_d11.9461395
X-RAY DIFFRACTIONf_chiral_restr0.075574
X-RAY DIFFRACTIONf_plane_restr0.008726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3031-1.31850.257650.1511289X-RAY DIFFRACTION36
1.3185-1.33450.207760.16551507X-RAY DIFFRACTION43
1.3345-1.35140.2293810.15211558X-RAY DIFFRACTION44
1.3514-1.36920.2049680.16381672X-RAY DIFFRACTION48
1.3692-1.3880.2578860.16591739X-RAY DIFFRACTION49
1.388-1.40780.2099850.17051842X-RAY DIFFRACTION53
1.4078-1.42880.2557930.16091940X-RAY DIFFRACTION55
1.4288-1.45110.1975980.16822052X-RAY DIFFRACTION59
1.4511-1.47490.23751160.16272103X-RAY DIFFRACTION60
1.4749-1.50030.221030.16562310X-RAY DIFFRACTION65
1.5003-1.52760.21031210.16582457X-RAY DIFFRACTION70
1.5276-1.5570.21261520.16782535X-RAY DIFFRACTION73
1.557-1.58880.22111560.17192644X-RAY DIFFRACTION76
1.5888-1.62330.21751580.17512774X-RAY DIFFRACTION80
1.6233-1.66110.20251760.17592939X-RAY DIFFRACTION84
1.6611-1.70260.24551440.16713048X-RAY DIFFRACTION87
1.7026-1.74860.24171840.16533096X-RAY DIFFRACTION89
1.7486-1.80010.19831800.16523223X-RAY DIFFRACTION92
1.8001-1.85820.191630.15723236X-RAY DIFFRACTION92
1.8582-1.92460.20551740.14953264X-RAY DIFFRACTION93
1.9246-2.00160.17621850.1423298X-RAY DIFFRACTION94
2.0016-2.09260.18971710.14833326X-RAY DIFFRACTION95
2.0926-2.20290.17361700.14243367X-RAY DIFFRACTION95
2.2029-2.34090.19351980.15473335X-RAY DIFFRACTION96
2.3409-2.52150.17782070.16553350X-RAY DIFFRACTION96
2.5215-2.7750.2311740.17113379X-RAY DIFFRACTION96
2.775-3.17590.17692020.16483351X-RAY DIFFRACTION96
3.1759-3.9990.17861600.16813284X-RAY DIFFRACTION93
3.999-26.21220.23551530.24412843X-RAY DIFFRACTION81

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