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- PDB-1a15: SDF-1ALPHA -

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Basic information

Entry
Database: PDB / ID: 1a15
TitleSDF-1ALPHA
ComponentsSTROMAL DERIVED FACTOR-1ALPHA
KeywordsCHEMOKINE / HUMAN STROMAL CELL-DERIVED FACTOR-1ALPHA
Function / homology
Function and homology information


chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / positive regulation of cell adhesion / positive regulation of T cell migration / animal organ regeneration / Nuclear signaling by ERBB4 / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / cell chemotaxis / adult locomotory behavior / axon guidance / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / chemotaxis / integrin binding / G alpha (i) signalling events / collagen-containing extracellular matrix / Estrogen-dependent gene expression / response to hypoxia / cell adhesion / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / signal transduction / extracellular exosome / extracellular region
Similarity search - Function
Stromal cell-derived factor 1 / CXC Chemokine domain / 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
Stromal cell-derived factor 1
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR WITH ANOMALOUS SCATTERING (MIRAS) / Resolution: 2.2 Å
AuthorsDealwis, C.G. / Fernandez, E.J. / Lolis, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1alpha, a potent ligand for the HIV-1 "fusin" coreceptor.
Authors: Dealwis, C. / Fernandez, E.J. / Thompson, D.A. / Simon, R.J. / Siani, M.A. / Lolis, E.
History
DepositionDec 22, 1997Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STROMAL DERIVED FACTOR-1ALPHA
B: STROMAL DERIVED FACTOR-1ALPHA
A: SULFATE ION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7093
Polymers15,6132
Non-polymers961
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-19 kcal/mol
Surface area8170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.840, 50.470, 64.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein STROMAL DERIVED FACTOR-1ALPHA / SDF-1


Mass: 7806.254 Da / Num. of mol.: 2 / Mutation: N33A / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / References: UniProt: P48061
#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.: 86 / 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: 2.22 Å3/Da / Density % sol: 35 %
Crystal growMethod: vapor diffusion / pH: 8.5
Details: PROTEIN CONCENTRATION 10MG/ML. WELL SOLUTION 1.9M AMMONIUM SULFATE 0.1M TRIS-HCL PH 8.5. CRYSTALLIZED USING VAPOR DIFFUSION., vapor diffusion
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
21.9 Mammonium sulfate1reservoir
30.1 MTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.95
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 8725 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 3.1 / % possible all: 99
Reflection
*PLUS
Num. measured all: 22469

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
RefinementMethod to determine structure: MIR WITH ANOMALOUS SCATTERING (MIRAS)
Resolution: 2.2→5 Å / Cross valid method: THROUGHOUT / σ(F): 3
Details: BULK SOLVENT CORRECTION WAS USED DURING SLOWCOOL AND POSITIONAL REFINEMENT IN XPLOR BETWEEN 25-2.2 ANGSTROM RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.298 575 10 %RANDOM
Rwork0.233 ---
obs0.233 5753 95 %-
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 5 64 1059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3 52 9 %
Rwork0.26 85 -
obs--92 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.3

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