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- PDB-5zxe: Structure of a consensus sequence derived from the FGF family -

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Basic information

Entry
Database: PDB / ID: 5zxe
TitleStructure of a consensus sequence derived from the FGF family
ComponentsConsensus sequence based basic form of fibroblast growth factor
KeywordsCELL CYCLE / FGF / basic form
Function / homologyTrefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsTripathi, S.K. / Mandalaparthy, V. / Ramaswamy, S. / Gosavi, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other privateEMR/2016/003885 India
Citation
Journal: To be published
Title: Structure of a consensus sequence derived from the FGF family
Authors: Tripathi, S.K. / Mandalaparthy, V. / Gosavi, S.
#1: Journal: J Tissue Eng / Year: 2010
Title: Fibroblast growth factors: biology, function, and application for tissue regeneration
Authors: Yun, Y.R. / Won, J.E. / Jeon, E. / Lee, S. / Kang, W. / Jo, H. / Jang, J.H. / Shin, U.S. / Kim, H.W.
History
DepositionMay 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Consensus sequence based basic form of fibroblast growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3076
Polymers14,9681
Non-polymers3395
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.718, 45.910, 90.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Consensus sequence based basic form of fibroblast growth factor


Mass: 14968.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria)

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Non-polymers , 5 types, 183 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: PEG 8000, Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 28, 2018
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.24→45.91 Å / Num. obs: 42829 / % possible obs: 99.2 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.03 / Rrim(I) all: 0.068 / Net I/σ(I): 12 / Num. measured all: 217407 / Scaling rejects: 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.24-1.264.40.94820480.6970.4841.07298.3
6.79-45.914.80.0283260.9990.0140.03199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.93 Å45.93 Å
Translation4.93 Å45.93 Å

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Processing

Software
NameVersionClassificationNB
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FGF

2fgf


Resolution: 1.3→45.435 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 1134 3.12 %RANDOM
Rwork0.1712 ---
obs0.1722 36301 96.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→45.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 19 178 1249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051128
X-RAY DIFFRACTIONf_angle_d0.771517
X-RAY DIFFRACTIONf_dihedral_angle_d16.609448
X-RAY DIFFRACTIONf_chiral_restr0.078154
X-RAY DIFFRACTIONf_plane_restr0.004196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.35920.33051240.24973852X-RAY DIFFRACTION86
1.3592-1.43080.27911430.24064445X-RAY DIFFRACTION99
1.4308-1.52050.27191420.22814399X-RAY DIFFRACTION98
1.5205-1.63790.22551450.15724497X-RAY DIFFRACTION100
1.6379-1.80270.2161450.15074512X-RAY DIFFRACTION100
1.8027-2.06360.21481400.17914329X-RAY DIFFRACTION95
2.0636-2.59990.18781410.1824384X-RAY DIFFRACTION95
2.5999-45.46280.17251540.15024749X-RAY DIFFRACTION99

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