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- PDB-1rfx: Crystal Structure of resisitin -

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Basic information

Entry
Database: PDB / ID: 1rfx
TitleCrystal Structure of resisitin
ComponentsResistin
KeywordsHORMONE/GROWTH FACTOR / HORMONE / GLUCOSE UPTAKE / RESISTIN/FIZZ FAMILY / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Neutrophil degranulation / hormone activity / extracellular space / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #200 / Resistin head domain / Resistin-like molecule hormone family / Resistin-like superfamily / Resistin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Resistin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsPatel, S.D. / Rajala, M.W. / Scherer, P.E. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Science / Year: 2004
Title: Disulfide-dependent multimeric assembly of resistin family hormones
Authors: Patel, S.D. / Rajala, M.W. / Rossetti, L. / Scherer, P.E. / Shapiro, L.
History
DepositionNov 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_special_symmetry / struct_site
Item: _audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Resistin
B: Resistin
C: Resistin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,60823
Polymers30,5483
Non-polymers1,06020
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-133 kcal/mol
Surface area14470 Å2
MethodPISA
2
A: Resistin
B: Resistin
C: Resistin
hetero molecules

A: Resistin
B: Resistin
C: Resistin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,21646
Polymers61,0976
Non-polymers2,11940
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area18600 Å2
ΔGint-292 kcal/mol
Surface area26540 Å2
MethodPISA
3
A: Resistin
hetero molecules

A: Resistin
hetero molecules

B: Resistin
C: Resistin
hetero molecules

B: Resistin
C: Resistin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,21646
Polymers61,0976
Non-polymers2,11940
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation5_545x+1/2,y-1/2,z1
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area13820 Å2
ΔGint-219 kcal/mol
Surface area31320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.298, 174.670, 90.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-82-

TRP

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Resistin / Cysteine-rich secreted protein FIZZ3 / Adipose tissue-specific secretory factor / ADSF / Adipose- ...Cysteine-rich secreted protein FIZZ3 / Adipose tissue-specific secretory factor / ADSF / Adipose-specific cysteine-rich secreted protein A12-alpha


Mass: 10182.790 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RETN / Plasmid: pFM1 / Production host: Homo sapiens (human) / References: UniProt: Q99P87

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Non-polymers , 5 types, 225 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 2
Details: 0.1M Sodium acetate, 8% PEG 4000, 0.1M Potassium Chloride, pH 2., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.54975 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54975 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 24119 / Num. obs: 24119 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 25.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 9.6 / % possible all: 95.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.002→14.86 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.109 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21597 1128 4.8 %RANDOM
Rwork0.17724 ---
all0.17915 22280 --
obs0.17915 22280 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.002→14.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 56 205 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212104
X-RAY DIFFRACTIONr_bond_other_d0.0020.021883
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9482850
X-RAY DIFFRACTIONr_angle_other_deg1.21434416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7072574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52415360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.908159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02377
X-RAY DIFFRACTIONr_nbd_refined0.2140.2384
X-RAY DIFFRACTIONr_nbd_other0.2010.21821
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21234
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3790.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7921.51439
X-RAY DIFFRACTIONr_mcbond_other0.1571.5546
X-RAY DIFFRACTIONr_mcangle_it1.3122189
X-RAY DIFFRACTIONr_scbond_it1.7923829
X-RAY DIFFRACTIONr_scangle_it2.5524.5661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.236 76
Rwork0.168 1571
obs-1571
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)
13.452-0.1021-0.1711.41110.16832.6040.0523-0.32750.53790.2021-0.06410.0224-0.1458-0.06260.01180.1594-0.0131-0.00290.1809-0.06690.0617-14.98749.53511.45
22.50890.43910.06383.1166-1.07381.25690.10540.1080.2124-0.0531-0.07770.028-0.02940.0298-0.02770.1606-0.00850.01430.1606-0.0239-0.0059-2.68949.749-1.618
32.94611.4653-0.54953.38970.58462.13260.1391-0.20090.12770.2428-0.10180.0417-0.0807-0.0097-0.03730.18640.0016-0.01130.176-0.0264-0.01931.65651.32413.042
41.0676-1.29980.145615.1618-1.70281.3874-0.13290.0353-0.3206-0.18850.0972-0.91470.18820.0160.03560.19390.0205-0.03120.1023-0.04010.2660.9713.6351.958
51.25935.18891.205921.53794.54122.32270.1456-0.1716-0.20330.9618-0.46320.7360.4543-0.02630.31760.2407-0.01870.08140.06910.01470.3164-4.9711.348.208
60.66-3.6006-1.884225.02111.06547.6661-0.031-0.1908-0.3148-0.5869-0.34060.9487-0.0193-0.11430.37170.1328-0.0143-0.05450.0623-0.01220.2728-7.47214.341.229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 9431 - 94
2X-RAY DIFFRACTION2BB31 - 9431 - 94
3X-RAY DIFFRACTION3CC31 - 9431 - 94
4X-RAY DIFFRACTION4AA6 - 306 - 30
5X-RAY DIFFRACTION5BB6 - 306 - 30
6X-RAY DIFFRACTION6CC6 - 306 - 30

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