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- PDB-1bff: THE 154 AMINO ACID FORM OF HUMAN BASIC FIBROBLAST GROWTH FACTOR -

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Basic information

Entry
Database: PDB / ID: 1bff
TitleTHE 154 AMINO ACID FORM OF HUMAN BASIC FIBROBLAST GROWTH FACTOR
ComponentsBASIC FIBROBLAST GROWTH FACTOR
KeywordsGROWTH FACTOR
Function / homology
Function and homology information


growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / response to wortmannin / positive regulation of cell fate specification / regulation of cell migration involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / response to wortmannin / positive regulation of cell fate specification / regulation of cell migration involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / chondroblast differentiation / lymphatic endothelial cell migration / negative regulation of fibroblast growth factor receptor signaling pathway / chemokine binding / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / angiogenesis involved in coronary vascular morphogenesis / Formation of the nephric duct / positive regulation of epithelial tube formation / stem cell development / regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cerebellar granule cell precursor proliferation / receptor-receptor interaction / negative regulation of wound healing / hyaluronan catabolic process / inner ear auditory receptor cell differentiation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / positive regulation of stem cell differentiation / Phospholipase C-mediated cascade; FGFR3 / cerebellar granule cell precursor proliferation / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / embryonic morphogenesis / behavioral response to ethanol / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / mammary gland epithelial cell differentiation / Phospholipase C-mediated cascade; FGFR4 / glial cell differentiation / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / paracrine signaling / Developmental Lineage of Pancreatic Acinar Cells / embryo development ending in birth or egg hatching / negative regulation of fibroblast migration / positive regulation of blood vessel branching / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / histone H3K9me2/3 reader activity / cell migration involved in sprouting angiogenesis / endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of DNA biosynthetic process / branching involved in ureteric bud morphogenesis / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / Syndecan interactions / PI-3K cascade:FGFR2 / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / positive regulation of sprouting angiogenesis / chemoattractant activity / positive regulation of MAP kinase activity / positive regulation of cell division / negative regulation of blood vessel endothelial cell migration / Non-integrin membrane-ECM interactions / PI3K Cascade / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / neuroblast proliferation / regulation of angiogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / response to axon injury / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / negative regulation of stem cell proliferation / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR3 signaling / positive regulation of vascular associated smooth muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / PHOSPHATE ION / Fibroblast growth factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2 Å
AuthorsKastrup, J.S. / Eriksson, E.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1997
Title: X-ray structure of the 154-amino-acid form of recombinant human basic fibroblast growth factor. comparison with the truncated 146-amino-acid form.
Authors: Kastrup, J.S. / Eriksson, E.S. / Dalboge, H. / Flodgaard, H.
History
DepositionDec 6, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: BASIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9733
Polymers14,8001
Non-polymers1732
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.800, 33.300, 36.500
Angle α, β, γ (deg.)64.10, 73.00, 76.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein BASIC FIBROBLAST GROWTH FACTOR / BFGF


Mass: 14800.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHD329 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P09038
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: THE PROTEIN WAS CRYSTALLIZED FROM 30-40 % PEG1000 AND 0.2-0.3 % 2-MERCAPTOETHANOL BY THE HANGING DROP VAPOR DIFFUSION METHOD., pH 7.5, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
215-20 %PEG10001drop
30.1-0.15 %beta-mercaptoethanol1drop
430-40 %PEG10001reservoir
50.2-0.3 %beta-mercaptoethanol1reservoir
1hbFGF1541drop0.003-0.005ml

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 1, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 7035 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.047 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.201 / % possible all: 46
Reflection
*PLUS
Num. measured all: 15506 / Rmerge(I) obs: 0.043

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Processing

Software
NameVersionClassification
TNTrefinement
XUONG-HAMLIN(DETECTOR SYSTEM)data reduction
XUONG-HAMLIN(DETECTOR SYSTEM)data scaling
TNTphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 4FGF

4fgf


Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: THE B-FACTORS WERE REFINED USING PROLSQ. THERE IS ONE RESIDUE (SER 151) WITH DEVIATING PHI, PSI ANGLES IN THE RAMACHANDRAN PLOT.
RfactorNum. reflection% reflection
Rwork0.19 --
obs-7035 84 %
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 9 67 1115
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0210691
X-RAY DIFFRACTIONt_angle_deg2.714252
X-RAY DIFFRACTIONt_dihedral_angle_d23.66472
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.014232.5
X-RAY DIFFRACTIONt_gen_planes0.0181555.5
X-RAY DIFFRACTIONt_it2
X-RAY DIFFRACTIONt_nbd0.0223520
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0142.5
X-RAY DIFFRACTIONt_plane_restr0.0185.5

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