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- PDB-1ccd: REFINED STRUCTURE OF RAT CLARA CELL 17 KDA PROTEIN AT 3.0 ANGSTRO... -

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Basic information

Entry
Database: PDB / ID: 1ccd
TitleREFINED STRUCTURE OF RAT CLARA CELL 17 KDA PROTEIN AT 3.0 ANGSTROMS RESOLUTION
ComponentsCLARA CELL 17 kD PROTEIN
KeywordsPHOSPHOLIPASE A2 INHIBITOR
Function / homology
Function and homology information


polychlorinated biphenyl binding / negative regulation of interleukin-4 production / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / phospholipase A2 inhibitor activity / response to silicon dioxide / response to ozone / response to fibroblast growth factor / negative regulation of type II interferon production / T cell proliferation ...polychlorinated biphenyl binding / negative regulation of interleukin-4 production / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / phospholipase A2 inhibitor activity / response to silicon dioxide / response to ozone / response to fibroblast growth factor / negative regulation of type II interferon production / T cell proliferation / negative regulation of T cell proliferation / response to cytokine / regulation of mRNA stability / response to glucocorticoid / secretory granule / nuclear envelope / regulation of inflammatory response / response to lipopolysaccharide / response to xenobiotic stimulus / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / cytoplasm
Similarity search - Function
Secretoglobin / Uteroglobin / Secretoglobin family 1C-like / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Uteroglobin / Uteroglobin / Secretoglobin superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsUmland, T.C. / Swaminathan, S. / Furey, W. / Singh, G. / Pletcher, J. / Sax, M.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Refined structure of rat Clara cell 17 kDa protein at 3.0 A resolution.
Authors: Umland, T.C. / Swaminathan, S. / Furey, W. / Singh, G. / Pletcher, J. / Sax, M.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization and Preliminary X-Ray Study of Rat Clara Cell 10,000 MR Protein
Authors: Swaminathan, S. / Furey, W. / Pletcher, J. / Katyal, S. / Singh, G. / Sax, M.
History
DepositionSep 17, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLARA CELL 17 kD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5722
Polymers8,4761
Non-polymers961
Water00
1
A: CLARA CELL 17 kD PROTEIN
hetero molecules

A: CLARA CELL 17 kD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1434
Polymers16,9512
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3000 Å2
ΔGint-35 kcal/mol
Surface area9220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.070, 52.070, 109.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CLARA CELL 17 kD PROTEIN


Mass: 8475.677 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P17559
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Compound detailsTHE AMINO ACID SEQUENCE OF RAT CLARA CELL 17 KDA PROTEIN IS 55.7 PERCENT IDENTICAL TO THAT OF ...THE AMINO ACID SEQUENCE OF RAT CLARA CELL 17 KDA PROTEIN IS 55.7 PERCENT IDENTICAL TO THAT OF RABBIT UTEROGLOBIN. PRIOR TO THE DETERMINATION OF THE SEQUENCE OF CLARA CELL 17 KDA PROTEIN, IT HAD BEEN REFERRED TO IN THE LITERATURE AS CLARA CELL 10 KDA PROTEIN BASED ON ITS ESTIMATED MOLECULAR WEIGHT. THE AMINO ACID RESIDUES OF RAT CLARA CELL 17 KDA PROTEIN HAVE BEEN NUMBERED SO AS TO EMPHASIZE ITS SEQUENCE HOMOLOGY WITH RABBIT UTEROGLOBIN.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal grow
*PLUS
pH: 7.1 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 mg/mlprotein1drop0.040ml
260 %(w/v)satammonium sulphate1drop0.005ml
310 mMTris-HCl1drop
460 %satammonium sulfate1reservoir
510 mg/mlTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 9999 Å / Num. obs: 1733 / % possible obs: 85 % / Rmerge(I) obs: 2 / Rmerge F obs: 0.117
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.4 Å / % possible obs: 63.3 % / Num. unique obs: 381 / Num. measured obs: 602

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Processing

Software
NameClassification
X-PLORmodel building
GPRLSArefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.225 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms594 0 5 0 599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0620.045
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.2840.2
X-RAY DIFFRACTIONp_singtor_nbd0.2160.3
X-RAY DIFFRACTIONp_multtor_nbd0.2480.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1740.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.65
X-RAY DIFFRACTIONp_staggered_tor26.315
X-RAY DIFFRACTIONp_orthonormal_tor32.215
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 1661 / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 7.23 Å2

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