HEADER CELL ADHESION 06-SEP-18 6MEQ TITLE PCDHGB3 EC1-4 IN 50 MM HEPES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTOCADHERIN GAMMA-B3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PCDH-GAMMA-B3; 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: PCDHGB3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS CELL-ADHESION, NEURONAL SELF-AVOIDANCE, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR J.M.NICOLUDIS,R.GAUDET REVDAT 3 11-OCT-23 6MEQ 1 LINK REVDAT 2 18-SEP-19 6MEQ 1 JRNL REVDAT 1 04-SEP-19 6MEQ 0 JRNL AUTH J.M.NICOLUDIS,A.G.GREEN,S.WALUJKAR,E.J.MAY,M.SOTOMAYOR, JRNL AUTH 2 D.S.MARKS,R.GAUDET JRNL TITL INTERACTION SPECIFICITY OF CLUSTERED PROTOCADHERINS INFERRED JRNL TITL 2 FROM SEQUENCE COVARIATION AND STRUCTURAL ANALYSIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 17825 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31431536 JRNL DOI 10.1073/PNAS.1821063116 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13RC1_2961) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 11831 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1181 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 49.9268 - 5.7978 0.98 1474 166 0.1921 0.2493 REMARK 3 2 5.7978 - 4.6029 0.99 1425 158 0.1826 0.2028 REMARK 3 3 4.6029 - 4.0213 0.99 1393 159 0.1988 0.2392 REMARK 3 4 4.0213 - 3.6538 0.99 1402 155 0.2336 0.2800 REMARK 3 5 3.6538 - 3.3920 0.99 1377 152 0.2720 0.3232 REMARK 3 6 3.3920 - 3.1920 0.99 1391 150 0.2914 0.3799 REMARK 3 7 3.1920 - 3.0322 0.89 1232 137 0.3415 0.3834 REMARK 3 8 3.0322 - 2.9002 0.70 956 104 0.4055 0.4700 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 75.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.001 3287 REMARK 3 ANGLE : 0.377 4469 REMARK 3 CHIRALITY : 0.041 518 REMARK 3 PLANARITY : 0.003 596 REMARK 3 DIHEDRAL : 11.486 2010 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.1139 58.4307 32.1088 REMARK 3 T TENSOR REMARK 3 T11: 0.8550 T22: 0.6065 REMARK 3 T33: 0.7321 T12: 0.0581 REMARK 3 T13: -0.0958 T23: 0.0191 REMARK 3 L TENSOR REMARK 3 L11: 2.4681 L22: 3.5602 REMARK 3 L33: 7.4471 L12: 1.7620 REMARK 3 L13: 1.7122 L23: 1.9504 REMARK 3 S TENSOR REMARK 3 S11: -0.1137 S12: 0.0617 S13: -0.1945 REMARK 3 S21: -0.2332 S22: -0.1219 S23: -0.0415 REMARK 3 S31: 0.0607 S32: 0.1079 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 100 THROUGH 208 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.6317 24.5459 3.4028 REMARK 3 T TENSOR REMARK 3 T11: 0.9551 T22: 0.7341 REMARK 3 T33: 0.6065 T12: 0.0807 REMARK 3 T13: 0.0218 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 3.2569 L22: 6.0069 REMARK 3 L33: 1.6372 L12: -0.6850 REMARK 3 L13: -0.9668 L23: 2.4089 REMARK 3 S TENSOR REMARK 3 S11: -0.1227 S12: 0.0443 S13: -0.2702 REMARK 3 S21: 0.0417 S22: 0.1942 S23: -0.3031 REMARK 3 S31: -0.0478 S32: 0.3931 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 209 THROUGH 313 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.3690 -17.9577 -22.8084 REMARK 3 T TENSOR REMARK 3 T11: 1.0303 T22: 0.6089 REMARK 3 T33: 0.9855 T12: 0.0228 REMARK 3 T13: -0.0187 T23: -0.0285 REMARK 3 L TENSOR REMARK 3 L11: 2.0895 L22: 3.2631 REMARK 3 L33: 6.3710 L12: -1.5454 REMARK 3 L13: -1.5052 L23: 3.3118 REMARK 3 S TENSOR REMARK 3 S11: 0.0875 S12: -0.1235 S13: 0.0978 REMARK 3 S21: 0.2232 S22: 0.1024 S23: -0.3094 REMARK 3 S31: -0.1672 S32: 0.1751 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 314 THROUGH 416 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.1885 -55.4152 -53.1110 REMARK 3 T TENSOR REMARK 3 T11: 0.9075 T22: 0.7542 REMARK 3 T33: 0.6436 T12: -0.0525 REMARK 3 T13: 0.1403 T23: 0.0879 REMARK 3 L TENSOR REMARK 3 L11: 2.4404 L22: 4.7094 REMARK 3 L33: 5.7215 L12: -1.9974 REMARK 3 L13: -0.2252 L23: 4.2798 REMARK 3 S TENSOR REMARK 3 S11: 0.1214 S12: 0.0710 S13: -0.2018 REMARK 3 S21: 0.1955 S22: -0.4419 S23: 0.0469 REMARK 3 S31: 0.4885 S32: 0.0935 S33: 0.0001 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6MEQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000236768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 70 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11833 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 49.919 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5K8R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM HEPES PH7, 10% PEG 5000MME, 4% REMARK 280 ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.42850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.42850 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 1.000000 0.000000 0.000000 63.40550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 81.45600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 63.40550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 81.45600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.42850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 63.40550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 81.45600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.42850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 63.40550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 81.45600 REMARK 290 SMTRY3 8 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 671 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 688 LIES ON A SPECIAL POSITION. 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 PHE A 26 -126.45 -102.73 REMARK 500 ASN A 35 76.08 51.44 REMARK 500 ASP A 293 -162.02 -122.52 REMARK 500 PRO A 361 42.04 -79.40 REMARK 500 ASP A 367 -70.25 -95.15 REMARK 500 THR A 368 -161.98 -109.32 REMARK 500 LYS A 397 40.33 -109.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 505 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 9 OE1 REMARK 620 2 GLU A 10 OE2 87.0 REMARK 620 3 ASP A 61 OD1 87.0 74.6 REMARK 620 4 GLU A 63 OE1 80.1 146.4 73.8 REMARK 620 5 ASP A 98 OD2 99.8 92.9 165.6 119.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 506 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 9 OE2 REMARK 620 2 GLU A 63 OE1 82.9 REMARK 620 3 GLU A 63 OE2 102.8 45.2 REMARK 620 4 ASP A 95 OD1 78.8 110.1 74.8 REMARK 620 5 ILE A 96 O 90.0 162.0 152.7 84.4 REMARK 620 6 ASP A 98 OD1 97.3 89.9 126.3 158.7 74.6 REMARK 620 7 ASP A 131 OD1 172.6 91.6 69.8 98.5 96.7 87.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 97 OD1 REMARK 620 2 ASN A 99 O 93.2 REMARK 620 3 ASP A 129 OD1 152.3 72.4 REMARK 620 4 ASP A 129 OD2 157.0 82.0 46.5 REMARK 620 5 ASP A 131 OD2 83.5 75.4 70.2 116.5 REMARK 620 6 ASN A 135 O 98.5 167.5 98.5 85.6 110.0 REMARK 620 7 ASP A 186 OD2 67.2 104.3 138.5 92.1 150.7 76.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 509 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 114 OE2 REMARK 620 2 GLU A 173 OE1 102.7 REMARK 620 3 GLU A 173 OE2 149.2 50.8 REMARK 620 4 ASP A 204 OD1 96.4 116.1 85.2 REMARK 620 5 ALA A 205 O 62.2 155.4 148.2 86.1 REMARK 620 6 ASP A 207 OD1 80.9 95.9 113.5 147.5 63.8 REMARK 620 7 ASP A 240 OD1 135.3 109.0 74.4 97.1 76.4 65.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 507 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 171 OD1 REMARK 620 2 GLU A 173 OE1 76.8 REMARK 620 3 ASP A 207 OD2 98.0 92.0 REMARK 620 4 HOH A 638 O 84.4 161.0 92.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 206 OD1 REMARK 620 2 ASN A 208 O 107.8 REMARK 620 3 ASP A 238 OD1 146.4 75.5 REMARK 620 4 ASP A 238 OD2 148.4 102.3 51.6 REMARK 620 5 ASP A 240 OD2 69.8 73.6 79.6 129.4 REMARK 620 6 ASN A 244 O 84.0 157.3 84.0 71.3 93.4 REMARK 620 7 ASP A 293 OD2 75.4 109.2 136.4 86.0 143.9 92.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 223 OE1 REMARK 620 2 GLU A 223 OE2 44.9 REMARK 620 3 GLU A 280 OE1 72.8 79.2 REMARK 620 4 GLU A 280 OE2 118.5 105.6 46.4 REMARK 620 5 ASP A 309 OD1 118.8 73.9 97.0 69.0 REMARK 620 6 GLU A 310 O 95.7 89.9 167.9 143.9 85.0 REMARK 620 7 ASP A 312 OD1 63.2 103.2 105.4 132.6 156.6 71.7 REMARK 620 8 ASP A 345 OD1 145.7 169.1 105.1 72.0 95.5 86.6 85.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 508 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 223 OE1 REMARK 620 2 ASP A 278 OD1 102.6 REMARK 620 3 GLU A 280 OE1 83.6 63.4 REMARK 620 4 ASP A 312 OD2 68.3 164.3 125.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 311 OD1 REMARK 620 2 ASN A 313 O 86.3 REMARK 620 3 ASP A 343 OD1 154.4 68.2 REMARK 620 4 ASP A 343 OD2 136.8 94.6 47.7 REMARK 620 5 ASP A 345 OD2 69.0 73.8 100.0 69.9 REMARK 620 6 ASN A 349 O 100.3 161.0 103.2 68.3 91.8 REMARK 620 7 ASP A 396 OD2 81.4 89.7 100.3 141.7 146.7 108.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 509 DBREF 6MEQ A 1 414 UNP Q9Y5G1 PCDGF_HUMAN 31 444 SEQADV 6MEQ ALA A 415 UNP Q9Y5G1 EXPRESSION TAG SEQADV 6MEQ ALA A 416 UNP Q9Y5G1 EXPRESSION TAG SEQRES 1 A 416 GLU PRO ILE ARG TYR ALA ILE PRO GLU GLU LEU ASP ARG SEQRES 2 A 416 GLY SER LEU VAL GLY ASN LEU ALA LYS ASP LEU GLY PHE SEQRES 3 A 416 GLY VAL GLY ASP LEU PRO THR ARG ASN LEU ARG VAL ILE SEQRES 4 A 416 ALA GLU LYS LYS PHE PHE THR VAL SER PRO GLU ASN GLY SEQRES 5 A 416 ASN LEU LEU VAL SER ASP ARG ILE ASP ARG GLU GLU ILE SEQRES 6 A 416 CYS GLY LYS LYS SER THR CYS VAL LEU GLU PHE GLU MET SEQRES 7 A 416 VAL ALA GLU LYS PRO LEU ASN PHE PHE HIS VAL THR VAL SEQRES 8 A 416 LEU ILE GLN ASP ILE ASN ASP ASN PRO PRO THR PHE SER SEQRES 9 A 416 GLN ASN ILE THR GLU LEU GLU ILE SER GLU LEU ALA LEU SEQRES 10 A 416 THR GLY ALA THR PHE ALA LEU GLU SER ALA GLN ASP PRO SEQRES 11 A 416 ASP VAL GLY VAL ASN SER LEU GLN GLN TYR TYR LEU SER SEQRES 12 A 416 PRO ASP PRO HIS PHE SER LEU ILE GLN LYS GLU ASN LEU SEQRES 13 A 416 ASP GLY SER ARG TYR PRO GLU LEU VAL LEU LYS ALA PRO SEQRES 14 A 416 LEU ASP ARG GLU GLU GLN PRO HIS HIS HIS LEU VAL LEU SEQRES 15 A 416 THR ALA VAL ASP GLY GLY GLU PRO SER ARG SER CYS THR SEQRES 16 A 416 THR GLN ILE ARG VAL ILE VAL ALA ASP ALA ASN ASP ASN SEQRES 17 A 416 PRO PRO VAL PHE THR GLN ASP MET TYR ARG VAL ASN VAL SEQRES 18 A 416 ALA GLU ASN LEU PRO ALA GLY SER SER VAL LEU LYS VAL SEQRES 19 A 416 MET ALA ILE ASP MET ASP GLU GLY ILE ASN ALA GLU ILE SEQRES 20 A 416 ILE TYR ALA PHE ILE ASN ILE GLY LYS GLU VAL ARG GLN SEQRES 21 A 416 LEU PHE LYS LEU ASP SER LYS THR GLY GLU LEU THR THR SEQRES 22 A 416 ILE GLY GLU LEU ASP PHE GLU GLU ARG ASP SER TYR THR SEQRES 23 A 416 ILE GLY VAL GLU ALA LYS ASP GLY GLY HIS HIS THR ALA SEQRES 24 A 416 TYR CYS LYS VAL GLN ILE ASP ILE SER ASP GLU ASN ASP SEQRES 25 A 416 ASN ALA PRO GLU ILE THR LEU ALA SER GLU SER GLN HIS SEQRES 26 A 416 ILE GLN GLU ASP ALA GLU LEU GLY THR ALA VAL ALA LEU SEQRES 27 A 416 ILE LYS THR HIS ASP LEU ASP SER GLY PHE ASN GLY GLU SEQRES 28 A 416 ILE LEU CYS GLN LEU LYS GLY ASN PHE PRO PHE LYS ILE SEQRES 29 A 416 VAL GLN ASP THR LYS ASN THR TYR ARG LEU VAL THR ASP SEQRES 30 A 416 GLY ALA LEU ASP ARG GLU GLN ILE PRO GLU TYR ASN VAL SEQRES 31 A 416 THR ILE THR ALA THR ASP LYS GLY ASN PRO PRO LEU SER SEQRES 32 A 416 SER SER LYS THR ILE THR LEU HIS ILE LEU ASP ALA ALA HET CA A 501 1 HET CA A 502 1 HET CA A 503 1 HET CA A 504 1 HET CA A 505 1 HET CA A 506 1 HET CA A 507 1 HET CA A 508 1 HET CA A 509 1 HETNAM CA CALCIUM ION FORMUL 2 CA 9(CA 2+) FORMUL 11 HOH *92(H2 O) HELIX 1 AA1 LEU A 20 GLY A 25 1 6 HELIX 2 AA2 GLY A 27 GLY A 29 5 3 HELIX 3 AA3 ASP A 30 ASN A 35 1 6 HELIX 4 AA4 ASP A 61 CYS A 66 1 6 HELIX 5 AA5 VAL A 132 SER A 136 5 5 HELIX 6 AA6 GLU A 241 ALA A 245 5 5 HELIX 7 AA7 GLY A 255 GLN A 260 1 6 HELIX 8 AA8 SER A 346 GLY A 350 5 5 SHEET 1 AA1 4 ILE A 3 PRO A 8 0 SHEET 2 AA1 4 ASN A 85 GLN A 94 1 O LEU A 92 N TYR A 5 SHEET 3 AA1 4 VAL A 73 ALA A 80 -1 N MET A 78 O PHE A 87 SHEET 4 AA1 4 ARG A 37 ILE A 39 -1 N ARG A 37 O VAL A 79 SHEET 1 AA2 3 LEU A 16 ASN A 19 0 SHEET 2 AA2 3 ASN A 53 VAL A 56 -1 O LEU A 54 N GLY A 18 SHEET 3 AA2 3 PHE A 45 VAL A 47 -1 N THR A 46 O LEU A 55 SHEET 1 AA3 4 ILE A 107 SER A 113 0 SHEET 2 AA3 4 SER A 193 ALA A 203 1 O ALA A 203 N ILE A 112 SHEET 3 AA3 4 HIS A 177 ASP A 186 -1 N LEU A 182 O THR A 196 SHEET 4 AA3 4 GLN A 138 LEU A 142 -1 N TYR A 141 O THR A 183 SHEET 1 AA4 3 THR A 121 ALA A 123 0 SHEET 2 AA4 3 ARG A 160 LEU A 166 -1 O LEU A 164 N PHE A 122 SHEET 3 AA4 3 PHE A 148 GLU A 154 -1 N ILE A 151 O GLU A 163 SHEET 1 AA5 2 VAL A 211 PHE A 212 0 SHEET 2 AA5 2 ALA A 236 ILE A 237 -1 O ILE A 237 N VAL A 211 SHEET 1 AA6 4 MET A 216 VAL A 221 0 SHEET 2 AA6 4 THR A 298 ILE A 307 1 O ASP A 306 N VAL A 219 SHEET 3 AA6 4 SER A 284 LYS A 292 -1 N ILE A 287 O VAL A 303 SHEET 4 AA6 4 ILE A 248 ILE A 252 -1 N ALA A 250 O GLU A 290 SHEET 1 AA7 3 SER A 230 LYS A 233 0 SHEET 2 AA7 3 GLU A 270 THR A 273 -1 O LEU A 271 N VAL A 231 SHEET 3 AA7 3 PHE A 262 LEU A 264 -1 N LYS A 263 O THR A 272 SHEET 1 AA8 4 GLU A 316 SER A 321 0 SHEET 2 AA8 4 ALA A 335 HIS A 342 -1 O LEU A 338 N ALA A 320 SHEET 3 AA8 4 THR A 371 THR A 376 -1 O LEU A 374 N ALA A 337 SHEET 4 AA8 4 PHE A 362 GLN A 366 -1 N LYS A 363 O VAL A 375 SHEET 1 AA9 4 HIS A 325 GLN A 327 0 SHEET 2 AA9 4 SER A 403 LEU A 413 1 O LEU A 413 N ILE A 326 SHEET 3 AA9 4 GLU A 387 ASP A 396 -1 N TYR A 388 O LEU A 410 SHEET 4 AA9 4 ILE A 352 LYS A 357 -1 N LEU A 353 O THR A 395 SSBOND 1 CYS A 66 CYS A 72 1555 1555 2.03 LINK OE1 GLU A 9 CA CA A 505 1555 1555 2.88 LINK OE2 GLU A 9 CA CA A 506 1555 1555 2.49 LINK OE2 GLU A 10 CA CA A 505 1555 1555 2.91 LINK OD1 ASP A 61 CA CA A 505 1555 1555 2.50 LINK OE1 GLU A 63 CA CA A 505 1555 1555 2.52 LINK OE1 GLU A 63 CA CA A 506 1555 1555 3.07 LINK OE2 GLU A 63 CA CA A 506 1555 1555 2.42 LINK OD1 ASP A 95 CA CA A 506 1555 1555 2.58 LINK O ILE A 96 CA CA A 506 1555 1555 2.50 LINK OD1 ASN A 97 CA CA A 504 1555 1555 2.47 LINK OD2 ASP A 98 CA CA A 505 1555 1555 2.57 LINK OD1 ASP A 98 CA CA A 506 1555 1555 2.53 LINK O ASN A 99 CA CA A 504 1555 1555 2.56 LINK OE2 GLU A 114 CA CA A 509 1555 1555 2.43 LINK OD1 ASP A 129 CA CA A 504 1555 1555 2.97 LINK OD2 ASP A 129 CA CA A 504 1555 1555 2.46 LINK OD2 ASP A 131 CA CA A 504 1555 1555 2.44 LINK OD1 ASP A 131 CA CA A 506 1555 1555 2.59 LINK O ASN A 135 CA CA A 504 1555 1555 2.47 LINK OD1 ASP A 171 CA CA A 507 1555 1555 2.51 LINK OE1 GLU A 173 CA CA A 507 1555 1555 2.46 LINK OE1 GLU A 173 CA CA A 509 1555 1555 2.65 LINK OE2 GLU A 173 CA CA A 509 1555 1555 2.45 LINK OD2 ASP A 186 CA CA A 504 1555 1555 2.71 LINK OD1 ASP A 204 CA CA A 509 1555 1555 2.40 LINK O ALA A 205 CA CA A 509 1555 1555 2.95 LINK OD1 ASN A 206 CA CA A 501 1555 1555 2.40 LINK OD2 ASP A 207 CA CA A 507 1555 1555 2.49 LINK OD1 ASP A 207 CA CA A 509 1555 1555 2.37 LINK O ASN A 208 CA CA A 501 1555 1555 2.48 LINK OE1 GLU A 223 CA CA A 503 1555 1555 3.08 LINK OE2 GLU A 223 CA CA A 503 1555 1555 2.47 LINK OE1 GLU A 223 CA CA A 508 1555 1555 2.43 LINK OD1 ASP A 238 CA CA A 501 1555 1555 2.57 LINK OD2 ASP A 238 CA CA A 501 1555 1555 2.46 LINK OD2 ASP A 240 CA CA A 501 1555 1555 2.50 LINK OD1 ASP A 240 CA CA A 509 1555 1555 2.81 LINK O ASN A 244 CA CA A 501 1555 1555 2.58 LINK OD1 ASP A 278 CA CA A 508 1555 1555 2.50 LINK OE1 GLU A 280 CA CA A 503 1555 1555 2.98 LINK OE2 GLU A 280 CA CA A 503 1555 1555 2.48 LINK OE1 GLU A 280 CA CA A 508 1555 1555 2.93 LINK OD2 ASP A 293 CA CA A 501 1555 1555 2.83 LINK OD1 ASP A 309 CA CA A 503 1555 1555 2.82 LINK O GLU A 310 CA CA A 503 1555 1555 2.47 LINK OD1 ASN A 311 CA CA A 502 1555 1555 2.60 LINK OD1 ASP A 312 CA CA A 503 1555 1555 2.48 LINK OD2 ASP A 312 CA CA A 508 1555 1555 2.62 LINK O ASN A 313 CA CA A 502 1555 1555 2.53 LINK OD1 ASP A 343 CA CA A 502 1555 1555 2.87 LINK OD2 ASP A 343 CA CA A 502 1555 1555 2.47 LINK OD2 ASP A 345 CA CA A 502 1555 1555 2.73 LINK OD1 ASP A 345 CA CA A 503 1555 1555 2.58 LINK O ASN A 349 CA CA A 502 1555 1555 2.58 LINK OD2 ASP A 396 CA CA A 502 1555 1555 3.12 LINK CA CA A 507 O HOH A 638 1555 1555 2.51 CISPEP 1 LYS A 82 PRO A 83 0 -3.12 CISPEP 2 GLU A 189 PRO A 190 0 -0.14 CISPEP 3 ASN A 399 PRO A 400 0 -0.58 SITE 1 AC1 6 ASN A 206 ASN A 208 ASP A 238 ASP A 240 SITE 2 AC1 6 ASN A 244 ASP A 293 SITE 1 AC2 6 ASN A 311 ASN A 313 ASP A 343 ASP A 345 SITE 2 AC2 6 ASN A 349 ASP A 396 SITE 1 AC3 7 GLU A 223 GLU A 280 ASP A 309 GLU A 310 SITE 2 AC3 7 ASP A 312 ASN A 313 ASP A 345 SITE 1 AC4 6 ASN A 97 ASN A 99 ASP A 129 ASP A 131 SITE 2 AC4 6 ASN A 135 ASP A 186 SITE 1 AC5 5 GLU A 9 GLU A 10 ASP A 61 GLU A 63 SITE 2 AC5 5 ASP A 98 SITE 1 AC6 6 GLU A 9 GLU A 63 ASP A 95 ILE A 96 SITE 2 AC6 6 ASP A 98 ASP A 131 SITE 1 AC7 4 ASP A 171 GLU A 173 ASP A 207 HOH A 638 SITE 1 AC8 4 GLU A 223 ASP A 278 GLU A 280 ASP A 312 SITE 1 AC9 6 GLU A 114 GLU A 173 ASP A 204 ALA A 205 SITE 2 AC9 6 ASP A 207 ASP A 240 CRYST1 126.811 162.912 52.857 90.00 90.00 90.00 C 2 2 21 8 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 0.007886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006138 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018919 0.00000