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- PDB-1rh7: Crystal Structure of Resistin-like beta -

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Basic information

Entry
Database: PDB / ID: 1rh7
TitleCrystal Structure of Resistin-like beta
ComponentsResistin-like beta
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


response to bacterium / hormone activity / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3290 / 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
: / Resistin-like beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.106 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: Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _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
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 1.5Oct 30, 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-like beta
B: Resistin-like beta
C: Resistin-like beta
D: Resistin-like beta
E: Resistin-like beta
F: Resistin-like beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,59314
Polymers51,8586
Non-polymers1,7358
Water2,522140
1
A: Resistin-like beta
B: Resistin-like beta
C: Resistin-like beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0798
Polymers25,9293
Non-polymers1,1505
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-81 kcal/mol
Surface area11810 Å2
MethodPISA
2
D: Resistin-like beta
E: Resistin-like beta
F: Resistin-like beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5146
Polymers25,9293
Non-polymers5853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-86 kcal/mol
Surface area11650 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-183 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.604, 86.016, 283.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

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Components

#1: Protein
Resistin-like beta / RELMbeta / Cysteine-rich secreted protein FIZZ2 / Cysteine-rich secreted protein A12-beta


Mass: 8642.917 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RETNLB or FIZZ2 / Plasmid: pFM1 / Production host: Homo sapiens (human) / References: UniProt: Q99P86
#2: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.61 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.5M NaCl, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.06975 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: 1.06975 Å / Relative weight: 1
ReflectionResolution: 3.1→15 Å / Num. all: 13231 / Num. obs: 13231 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 20
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1304 / % possible all: 100

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Processing

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

1rgx


Resolution: 3.106→14.96 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.844 / SU B: 16.238 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 671 5.1 %RANDOM
Rwork0.20117 ---
all0.20431 12406 --
obs0.20431 12406 99.95 %-
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: 28.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 3.106→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 32 140 3475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213402
X-RAY DIFFRACTIONr_bond_other_d0.0020.022927
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9384627
X-RAY DIFFRACTIONr_angle_other_deg0.82636743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3065480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31321.97891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0315479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5321524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
X-RAY DIFFRACTIONr_nbd_refined0.2280.2803
X-RAY DIFFRACTIONr_nbd_other0.230.23239
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.22153
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3560.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6181.52428
X-RAY DIFFRACTIONr_mcbond_other0.0391.51013
X-RAY DIFFRACTIONr_mcangle_it1.13523778
X-RAY DIFFRACTIONr_scbond_it0.7631109
X-RAY DIFFRACTIONr_scangle_it1.2844.5849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.106→3.183 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.331 50
Rwork0.238 884
obs-884

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