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- PDB-2j7z: Crystal Structure of recombinant Human Stromal Cell-Derived Facto... -

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Basic information

Entry
Database: PDB / ID: 2j7z
TitleCrystal Structure of recombinant Human Stromal Cell-Derived Factor- 1alpha
ComponentsSTROMAL CELL-DERIVED FACTOR 1 ALPHA
KeywordsGROWTH FACTOR / ALTERNATIVE SPLICING / CXCR4 / CYTOKINE / REFOLDING / CHEMOTAXIS / SDF-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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRyu, E.K. / Kim, T.G. / Kwon, T.H. / Jung, I.D. / Ryu, D.W. / Park, Y.-M. / Ahn, K. / Ban, C.
CitationJournal: Proteins / Year: 2007
Title: Crystal Structure of Recombinant Human Stromal Cell-Derived Factor-1Alpha.
Authors: Ryu, E.K. / Kim, T.G. / Kwon, T.H. / Jung, I.D. / Ryu, D. / Park, Y. / Kim, J. / Ahn, K.H. / Ban, C.
History
DepositionOct 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: STROMAL CELL-DERIVED FACTOR 1 ALPHA
B: STROMAL CELL-DERIVED FACTOR 1 ALPHA


Theoretical massNumber of molelcules
Total (without water)15,9572
Polymers15,9572
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.215, 56.675, 71.629
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 CELL-DERIVED FACTOR 1 ALPHA / SDF-1 / CXCL12 / PRE-B CELL GROWTH-STIMULATING FACTOR / PBSF


Mass: 7978.460 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48061
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.08 %

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 15982 / % possible obs: 98 % / Observed criterion σ(I): 14.3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.06

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QG7

1qg7


Resolution: 1.95→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2466 1068 9.8 %
Rwork0.2133 --
obs0.2133 10504 96.1 %
Solvent computationBsol: 61.9145 Å2 / ksol: 0.391864 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.099 Å20 Å20 Å2
2--1.519 Å20 Å2
3---5.58 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 0 99 1217
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.65
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.74
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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