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- PDB-1rgx: Crystal Structure of resisitin -

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Basic information

Entry
Database: PDB / ID: 1rgx
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.787 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 13, 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: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Aug 23, 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)37,5143
Polymers37,5143
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-56 kcal/mol
Surface area13690 Å2
MethodPISA
2
A: Resistin
B: Resistin
C: Resistin

A: Resistin
B: Resistin
C: Resistin


Theoretical massNumber of molelcules
Total (without water)75,0286
Polymers75,0286
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area13940 Å2
ΔGint-143 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.021, 52.475, 96.609
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#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: 12504.670 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
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: 2.02 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 40% MPD, 8% PEG 5000MME, 0.2M MgCl2, 0.1M Na Acetate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.0542517 Å
DetectorType: MACSCIENCE / Detector: CCD / Date: Dec 2, 2000
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0542517 Å / Relative weight: 1
ReflectionResolution: 1.787→20 Å / Num. all: 23080 / Num. obs: 21591 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.3
Reflection shellResolution: 1.787→1.86 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.9999refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RFX

1rfx


Resolution: 1.787→17.82 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.541 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.154 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24494 1087 4.8 %RANDOM
Rwork0.20377 ---
all0.20577 21591 --
obs0.20577 21591 97.74 %-
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: 26.408 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.01 Å2
2---0.47 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.787→17.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 0 179 2179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212053
X-RAY DIFFRACTIONr_bond_other_d0.0070.021818
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9432789
X-RAY DIFFRACTIONr_angle_other_deg0.78534247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.195269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81124.16772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94815344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6931512
X-RAY DIFFRACTIONr_chiral_restr0.070.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
X-RAY DIFFRACTIONr_nbd_refined0.20.2428
X-RAY DIFFRACTIONr_nbd_other0.2020.21827
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.661.51426
X-RAY DIFFRACTIONr_mcbond_other0.0721.5555
X-RAY DIFFRACTIONr_mcangle_it0.99222164
X-RAY DIFFRACTIONr_scbond_it1.1673784
X-RAY DIFFRACTIONr_scangle_it1.6094.5625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.787→1.833 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.259 53
Rwork0.209 1467
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)
13.30771.2515-0.56351.1646-0.40761.4337-0.37910.6535-0.3096-0.17850.2765-0.24480.2391-0.21090.1027-0.0056-0.07730.11630.2807-0.0669-0.10145.315-1.3717.83
21.9403-0.2324-0.71580.6778-0.04043.1796-0.0964-0.3377-0.10820.03990.0395-0.06980.27680.50190.0569-0.04650.03480.03140.24760.0326-0.105110.153-4.68721.252
34.7232-0.5071-1.06030.43110.23430.95320.1974-0.27350.44420.00880.0169-0.0581-0.0699-0.0963-0.2143-0.01070.02080.06760.16160.0289-0.1294-3.6133.20926.365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 9426 - 114
2X-RAY DIFFRACTION2BB9 - 9429 - 114
3X-RAY DIFFRACTION3CC1 - 9421 - 114

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