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- PDB-9niu: Co-crystal structure of FABP7 in complex with PFO3TDA -

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Basic information

Entry
Database: PDB / ID: 9niu
TitleCo-crystal structure of FABP7 in complex with PFO3TDA
ComponentsFatty acid-binding protein, brain
KeywordsTRANSPORT PROTEIN / FABP7 / SGC / Structural Genomics / PSI-Biology / Structural Genomics Consortium
Function / homology
Function and homology information


NOTCH3 Intracellular Domain Regulates Transcription / Triglyceride catabolism / fatty acid transport / fatty acid binding / epithelial cell proliferation / nervous system development / negative regulation of cell population proliferation / lipid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
: / Fatty acid-binding protein, brain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYang, D. / Liu, J. / Zeng, H. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Peng, H. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To be published
Title: Co-crystal structure of FABP7 in complex with PFO3TDA
Authors: Yang, D. / Liu, J. / Zeng, H. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Peng, H. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionFeb 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, brain
B: Fatty acid-binding protein, brain
C: Fatty acid-binding protein, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1979
Polymers51,3253
Non-polymers1,8726
Water3,027168
1
A: Fatty acid-binding protein, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7323
Polymers17,1081
Non-polymers6242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7323
Polymers17,1081
Non-polymers6242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid-binding protein, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7323
Polymers17,1081
Non-polymers6242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.110, 125.822, 47.614
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fatty acid-binding protein, brain / Brain lipid-binding protein / BLBP / Brain-type fatty acid-binding protein / B-FABP / Fatty acid- ...Brain lipid-binding protein / BLBP / Brain-type fatty acid-binding protein / B-FABP / Fatty acid-binding protein 7 / Mammary-derived growth inhibitor related


Mass: 17108.281 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP7, BLBP, FABPB, MRG / Production host: Escherichia coli (E. coli) / References: UniProt: O15540
#2: Chemical ChemComp-A1BYP / difluoro{1,1,2,2-tetrafluoro-2-[1,1,2,2-tetrafluoro-2-(nonafluorobutoxy)ethoxy]ethoxy}acetic acid


Mass: 562.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10HF19O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350,12.5% v/v MPD, 0.03M of each halide, 0.1M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 31719 / % possible obs: 95.1 % / Redundancy: 4.3 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.024 / Rrim(I) all: 0.052 / Χ2: 1.398 / Net I/σ(I): 14.9 / Num. measured all: 135960
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.9330.2428820.9690.9920.140.2821.18854.4
1.93-1.973.30.22511820.9860.9960.1280.260.99870.4
1.97-2.013.50.22115100.9870.9970.1250.2550.96289.3
2.01-2.0540.22615400.9850.9960.1250.2591.02994.5
2.05-2.094.20.21616070.9760.9940.1170.2471.21996.9
2.09-2.144.30.18316470.990.9970.0980.2090.99398
2.14-2.194.30.1616330.9910.9980.0850.1821.07799.6
2.19-2.254.40.15316960.9910.9980.0820.1741.24899.8
2.25-2.324.40.13616290.9940.9980.0730.1551.1599.9
2.32-2.394.50.10616770.9960.9990.0560.121.185100
2.39-2.484.40.09816600.9960.9990.0520.1121.196100
2.48-2.584.50.08716690.9960.9990.0460.0991.278100
2.58-2.74.40.07316570.9970.9990.0390.0831.2899.9
2.7-2.844.40.06116570.9980.9990.0320.0691.398100
2.84-3.024.40.05116910.99810.0270.0581.487100
3.02-3.254.40.04316690.99810.0230.0491.724100
3.25-3.584.50.03416660.99910.0180.0391.84499.9
3.58-4.094.50.03416780.99910.0180.0391.972100
4.09-5.164.60.03316860.99810.0160.0372.01799.9
5.16-504.70.03316830.99910.0180.0381.97998.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.34 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1524 4.84 %RANDOM
Rwork0.22 ---
obs0.222 31489 94.4 %-
Displacement parametersBiso mean: 45.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.2151 Å20 Å2-1.407 Å2
2--9.5546 Å20 Å2
3----9.7697 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 1.9→27.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 114 168 3587
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013487HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14748HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1239SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes590HARMONIC5
X-RAY DIFFRACTIONt_it3487HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion17.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion448SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3967SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.92 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2926 -4.76 %
Rwork0.2701 600 -
all0.2711 630 -
obs--50.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.24750.65931.97716.65770.04692.3328-0.0766-0.21720.08710.5451-0.09340.1437-0.2164-0.17970.1699-0.12870.00850.0473-0.1753-0.0060.05468.562219.830610.7013
22.26910.92430.64935.32180.52741.86260.05820.046-0.1185-0.5521-0.0690.0005-0.06650.10360.0108-0.10220.0030.0215-0.20120.0120.0889-8.588741.4568-10.9578
31.8754-0.12130.78874.3309-0.4312.3820.1506-0.17120.0130.5514-0.0775-0.0461-0.1979-0.0809-0.0731-0.0922-0.0170.0532-0.1631-0.00190.06687.320661.907810.0493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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