HEADER SIGNALING PROTEIN 05-JUN-16 5KC5 TITLE CRYSTAL STRUCTURE OF THE CBLN1 C1Q DOMAIN TRIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEREBELLIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PRECEREBELLIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CBLN1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293S; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PHLSEC KEYWDS CEREBELLIN, C1Q, NEUROTRANSMISSION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.ELEGHEERT,J.E.CLAY,C.SIEBOLD,A.R.ARICESCU REVDAT 4 10-JAN-24 5KC5 1 HETSYN REVDAT 3 29-JUL-20 5KC5 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 28-SEP-16 5KC5 1 REVDAT 1 27-JUL-16 5KC5 0 JRNL AUTH J.ELEGHEERT,W.KAKEGAWA,J.E.CLAY,N.F.SHANKS,E.BEHIELS, JRNL AUTH 2 K.MATSUDA,K.KOHDA,E.MIURA,M.ROSSMANN,N.MITAKIDIS, JRNL AUTH 3 J.MOTOHASHI,V.T.CHANG,C.SIEBOLD,I.H.GREGER,T.NAKAGAWA, JRNL AUTH 4 M.YUZAKI,A.R.ARICESCU JRNL TITL STRUCTURAL BASIS FOR INTEGRATION OF GLUD RECEPTORS WITHIN JRNL TITL 2 SYNAPTIC ORGANIZER COMPLEXES. JRNL REF SCIENCE V. 353 295 2016 JRNL REFN ESSN 1095-9203 JRNL PMID 27418511 JRNL DOI 10.1126/SCIENCE.AAE0104 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1772 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 8497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 407 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 21.7477 - 3.3891 0.95 2737 133 0.1514 0.1704 REMARK 3 2 3.3891 - 2.6916 0.95 2672 130 0.2011 0.2323 REMARK 3 3 2.6916 - 2.3519 0.95 2656 144 0.2530 0.2961 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.1700 REMARK 3 OPERATOR: H,-H-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1120 REMARK 3 ANGLE : 0.559 1513 REMARK 3 CHIRALITY : 0.027 165 REMARK 3 PLANARITY : 0.002 195 REMARK 3 DIHEDRAL : 11.089 405 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINED WITH TWIN OPERATOR H, -H-K, -L REMARK 3 TO ACCOUNT FOR HIGHER P622 METRIC SYMMETRY REMARK 4 REMARK 4 5KC5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07300 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8497 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 1.26300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1GR3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM MALONATE PH 7.0, 20% REMARK 280 (W/V) POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C3). REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -41.71000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 72.24384 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -83.42000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 56 REMARK 465 THR A 57 REMARK 465 THR A 195 REMARK 465 LYS A 196 REMARK 465 HIS A 197 REMARK 465 HIS A 198 REMARK 465 HIS A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 REMARK 465 HIS A 202 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 92 55.93 -164.55 REMARK 500 ASN A 123 31.79 -159.01 REMARK 500 ASP A 145 119.53 -163.31 REMARK 500 REMARK 500 REMARK: NULL DBREF 5KC5 A 58 193 UNP P23435 CBLN1_HUMAN 58 193 SEQADV 5KC5 GLU A 56 UNP P23435 EXPRESSION TAG SEQADV 5KC5 THR A 57 UNP P23435 EXPRESSION TAG SEQADV 5KC5 GLY A 194 UNP P23435 EXPRESSION TAG SEQADV 5KC5 THR A 195 UNP P23435 EXPRESSION TAG SEQADV 5KC5 LYS A 196 UNP P23435 EXPRESSION TAG SEQADV 5KC5 HIS A 197 UNP P23435 EXPRESSION TAG SEQADV 5KC5 HIS A 198 UNP P23435 EXPRESSION TAG SEQADV 5KC5 HIS A 199 UNP P23435 EXPRESSION TAG SEQADV 5KC5 HIS A 200 UNP P23435 EXPRESSION TAG SEQADV 5KC5 HIS A 201 UNP P23435 EXPRESSION TAG SEQADV 5KC5 HIS A 202 UNP P23435 EXPRESSION TAG SEQRES 1 A 147 GLU THR GLY SER ALA LYS VAL ALA PHE SER ALA ILE ARG SEQRES 2 A 147 SER THR ASN HIS GLU PRO SER GLU MET SER ASN ARG THR SEQRES 3 A 147 MET ILE ILE TYR PHE ASP GLN VAL LEU VAL ASN ILE GLY SEQRES 4 A 147 ASN ASN PHE ASP SER GLU ARG SER THR PHE ILE ALA PRO SEQRES 5 A 147 ARG LYS GLY ILE TYR SER PHE ASN PHE HIS VAL VAL LYS SEQRES 6 A 147 VAL TYR ASN ARG GLN THR ILE GLN VAL SER LEU MET LEU SEQRES 7 A 147 ASN GLY TRP PRO VAL ILE SER ALA PHE ALA GLY ASP GLN SEQRES 8 A 147 ASP VAL THR ARG GLU ALA ALA SER ASN GLY VAL LEU ILE SEQRES 9 A 147 GLN MET GLU LYS GLY ASP ARG ALA TYR LEU LYS LEU GLU SEQRES 10 A 147 ARG GLY ASN LEU MET GLY GLY TRP LYS TYR SER THR PHE SEQRES 11 A 147 SER GLY PHE LEU VAL PHE PRO LEU GLY THR LYS HIS HIS SEQRES 12 A 147 HIS HIS HIS HIS HET NAG A 301 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 HOH *55(H2 O) HELIX 1 AA1 MET A 77 MET A 82 1 6 SHEET 1 AA1 5 GLN A 88 ILE A 93 0 SHEET 2 AA1 5 ALA A 63 ILE A 67 -1 N ILE A 67 O GLN A 88 SHEET 3 AA1 5 THR A 184 PRO A 192 -1 O GLY A 187 N PHE A 64 SHEET 4 AA1 5 GLY A 110 LYS A 120 -1 N SER A 113 O PHE A 188 SHEET 5 AA1 5 GLU A 151 MET A 161 -1 O ILE A 159 N TYR A 112 SHEET 1 AA2 5 PHE A 97 ASP A 98 0 SHEET 2 AA2 5 THR A 103 ILE A 105 -1 O THR A 103 N ASP A 98 SHEET 3 AA2 5 ARG A 166 ARG A 173 -1 O ALA A 167 N PHE A 104 SHEET 4 AA2 5 ILE A 127 LEU A 133 -1 N MET A 132 O TYR A 168 SHEET 5 AA2 5 TRP A 136 ALA A 143 -1 O TRP A 136 N LEU A 133 LINK ND2 ASN A 79 C1 NAG A 301 1555 1555 1.44 CRYST1 83.420 83.420 50.570 90.00 90.00 120.00 P 6 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011983 0.006919 0.000000 0.00000 SCALE2 0.000000 0.013837 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019782 0.00000