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- PDB-1b3a: TOTAL CHEMICAL SYNTHESIS AND HIGH-RESOLUTION CRYSTAL STRUCTURE OF... -

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Basic information

Entry
Database: PDB / ID: 1b3a
TitleTOTAL CHEMICAL SYNTHESIS AND HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE POTENT ANTI-HIV PROTEIN AOP-RANTES
ComponentsPROTEIN (RANTES)
KeywordsANTI-HIV PROTEIN / CHEMICAL PROTEIN SYNTHESIS / CHEMOKINE / HIV-1 / RANTES
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / chemokine receptor antagonist activity / phospholipase D-activating G protein-coupled receptor signaling pathway / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / receptor signaling protein tyrosine kinase activator activity ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / chemokine receptor antagonist activity / phospholipase D-activating G protein-coupled receptor signaling pathway / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / receptor signaling protein tyrosine kinase activator activity / CCR5 chemokine receptor binding / positive regulation of receptor signaling pathway via STAT / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of homotypic cell-cell adhesion / neutrophil activation / positive regulation of G protein-coupled receptor signaling pathway / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / chemokine-mediated signaling pathway / eosinophil chemotaxis / positive regulation of calcium ion transport / positive regulation of monocyte chemotaxis / cell surface receptor signaling pathway via STAT / positive regulation of innate immune response / chemokine activity / regulation of T cell activation / Chemokine receptors bind chemokines / dendritic cell chemotaxis / positive regulation of smooth muscle cell migration / negative regulation of G protein-coupled receptor signaling pathway / phospholipase activator activity / leukocyte cell-cell adhesion / negative regulation of viral genome replication / positive regulation of macrophage chemotaxis / chemoattractant activity / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / exocytosis / positive regulation of translational initiation / cellular response to interleukin-1 / host-mediated suppression of viral transcription / positive regulation of TOR signaling / positive regulation of T cell migration / positive regulation of viral genome replication / cellular response to fibroblast growth factor stimulus / positive regulation of T cell proliferation / positive regulation of smooth muscle cell proliferation / regulation of insulin secretion / positive regulation of cell adhesion / epithelial cell proliferation / positive regulation of epithelial cell proliferation / cellular response to virus / cellular response to type II interferon / response to toxic substance / response to virus / intracellular calcium ion homeostasis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to tumor necrosis factor / calcium ion transport / cell-cell signaling / G alpha (i) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PENTYLOXYAMINO-ACETALDEHYDE / C-C motif chemokine 5
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWilken, J. / Hoover, D. / Thompson, D.A. / Barlow, P.N. / Mcsparron, H. / Picard, L. / Wlodawer, A. / Lubkowski, J. / Kent, S.B.H.
CitationJournal: Chem.Biol. / Year: 1999
Title: Total chemical synthesis and high-resolution crystal structure of the potent anti-HIV protein AOP-RANTES.
Authors: Wilken, J. / Hoover, D. / Thompson, D.A. / Barlow, P.N. / McSparron, H. / Picard, L. / Wlodawer, A. / Lubkowski, J. / Kent, S.B.
History
DepositionDec 7, 1998Deposition site: NDB / Processing site: RCSB
Revision 1.0Apr 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RANTES)
B: PROTEIN (RANTES)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2258
Polymers15,5502
Non-polymers6756
Water3,999222
1
A: PROTEIN (RANTES)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2085
Polymers7,7751
Non-polymers4334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (RANTES)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0163
Polymers7,7751
Non-polymers2412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.635, 56.307, 94.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.993225, 0.114072, 0.022194), (0.079982, 0.532445, 0.842677), (0.084309, 0.838743, -0.537961)
Vector: 29.97141, -13.80924, 20.89648)

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Components

#1: Protein PROTEIN (RANTES)


Mass: 7774.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: OXIME LINK BETWEEN AOP GROUP AND PRO3 / References: UniProt: P13501
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AOP / PENTYLOXYAMINO-ACETALDEHYDE


Mass: 145.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsMODRES: 1B3A AOP A 1() AMINOOXYPENTANE LINKED TO PRO2 VIA OXIME BOND MODRES: 1B3A AOP B 1() ...MODRES: 1B3A AOP A 1() AMINOOXYPENTANE LINKED TO PRO2 VIA OXIME BOND MODRES: 1B3A AOP B 1() AMINOOXYPENTANE LINKED TO PRO2 VIA OXIME BOND

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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: 1.98 Å3/Da / Density % sol: 32.7 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMsodium acetate1drop
215 mg/mlprotein1drop
30.1 Mammonium sulfate1reservoir
4225 mMsodium succinate1reservoir
5275 mM2-(N-morpholino)ethanesulfonic acid1reservoir
615 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 17338 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.043 / Rsym value: 0.056 / Net I/σ(I): 31.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 7.5 / Rsym value: 0.25 / % possible all: 100
Reflection
*PLUS
Num. measured all: 74936
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
SHELXL-97refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Num. parameters: 5447 / Num. restraintsaints: 4683 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28 (1995) 53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 1696 10 %RANDOM
all0.175 16956 --
obs0.1673 -99.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL. 91 (1973) 201-228
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1358
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 40 223 1357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.072
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.167 / Rfactor Rwork: 0.1673
Solvent computation
*PLUS
Displacement parameters
*PLUS

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