HEADER CELL ADHESION 06-SEP-18 6MER 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 6MER 1 LINK REVDAT 2 18-SEP-19 6MER 1 JRNL REVDAT 1 04-SEP-19 6MER 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. 3.00 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 10826 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 : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1089 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 29.8358 - 5.9859 0.95 1284 142 0.1970 0.2370 REMARK 3 2 5.9859 - 4.7574 0.96 1220 139 0.1962 0.2526 REMARK 3 3 4.7574 - 4.1578 0.96 1227 131 0.1965 0.2344 REMARK 3 4 4.1578 - 3.7785 0.97 1219 140 0.2280 0.2783 REMARK 3 5 3.7785 - 3.5081 0.97 1207 137 0.2500 0.2967 REMARK 3 6 3.5081 - 3.3016 0.97 1201 137 0.2840 0.3640 REMARK 3 7 3.3016 - 3.1364 0.96 1202 131 0.3248 0.3470 REMARK 3 8 3.1364 - 3.0000 0.94 1177 132 0.3307 0.3950 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) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 82.12 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 3277 REMARK 3 ANGLE : 0.390 4455 REMARK 3 CHIRALITY : 0.042 516 REMARK 3 PLANARITY : 0.003 594 REMARK 3 DIHEDRAL : 11.090 2004 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 1:95)) REMARK 3 ORIGIN FOR THE GROUP (A): 45.8935 58.0718 32.3867 REMARK 3 T TENSOR REMARK 3 T11: 0.9319 T22: 0.8666 REMARK 3 T33: 0.9009 T12: 0.0464 REMARK 3 T13: -0.1360 T23: -0.0143 REMARK 3 L TENSOR REMARK 3 L11: 2.8375 L22: 1.9042 REMARK 3 L33: 5.3230 L12: 1.9386 REMARK 3 L13: 2.9284 L23: 2.3811 REMARK 3 S TENSOR REMARK 3 S11: -0.3339 S12: 0.1134 S13: 0.1696 REMARK 3 S21: -0.3049 S22: 0.1036 S23: -0.0308 REMARK 3 S31: -0.1174 S32: -0.0329 S33: -0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 96:208)) REMARK 3 ORIGIN FOR THE GROUP (A): 39.1637 25.1380 3.6818 REMARK 3 T TENSOR REMARK 3 T11: 0.9018 T22: 0.9385 REMARK 3 T33: 0.7765 T12: 0.0622 REMARK 3 T13: 0.0174 T23: -0.0563 REMARK 3 L TENSOR REMARK 3 L11: 3.4481 L22: 4.4635 REMARK 3 L33: 0.8645 L12: 0.3113 REMARK 3 L13: -0.1236 L23: 0.9395 REMARK 3 S TENSOR REMARK 3 S11: -0.0601 S12: 0.0922 S13: -0.1894 REMARK 3 S21: 0.0068 S22: -0.0599 S23: -0.0682 REMARK 3 S31: 0.0914 S32: 0.1924 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 209:313)) REMARK 3 ORIGIN FOR THE GROUP (A): 51.0247 -17.5956 -22.4330 REMARK 3 T TENSOR REMARK 3 T11: 0.9747 T22: 0.9135 REMARK 3 T33: 1.1476 T12: 0.0967 REMARK 3 T13: -0.0766 T23: -0.2686 REMARK 3 L TENSOR REMARK 3 L11: 1.3191 L22: 1.4361 REMARK 3 L33: 4.3912 L12: 0.3569 REMARK 3 L13: -1.0348 L23: 1.9136 REMARK 3 S TENSOR REMARK 3 S11: -0.2773 S12: -0.2798 S13: 0.0101 REMARK 3 S21: 0.4949 S22: -0.1563 S23: 0.3999 REMARK 3 S31: 0.2976 S32: -0.1704 S33: -0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 314:414)) REMARK 3 ORIGIN FOR THE GROUP (A): 58.8809 -54.3111 -52.3085 REMARK 3 T TENSOR REMARK 3 T11: 0.7755 T22: 0.7704 REMARK 3 T33: 0.7506 T12: -0.0235 REMARK 3 T13: 0.1295 T23: 0.0238 REMARK 3 L TENSOR REMARK 3 L11: 2.2150 L22: 4.6738 REMARK 3 L33: 3.8353 L12: -0.9535 REMARK 3 L13: -0.2142 L23: 1.2775 REMARK 3 S TENSOR REMARK 3 S11: -0.0856 S12: -0.1024 S13: -0.0835 REMARK 3 S21: 0.4188 S22: -0.2470 S23: 0.0902 REMARK 3 S31: 0.3129 S32: -0.0193 S33: -0.0000 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 6MER 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_1000236767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 77 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) : 1.07 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 : 10828 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.834 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.14360 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 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 (%): 58.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 7, 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 26.08000 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 26.08000 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 64.19500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 80.88500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 64.19500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 80.88500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.08000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 64.19500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 80.88500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.08000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 64.19500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 80.88500 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: 3940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 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 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 ALA A 415 REMARK 465 ALA A 416 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 35 71.53 51.98 REMARK 500 LYS A 82 72.09 54.36 REMARK 500 ASP A 240 -163.45 -79.66 REMARK 500 ASP A 293 -167.97 -116.33 REMARK 500 GLN A 324 49.21 37.94 REMARK 500 PRO A 361 46.92 -75.06 REMARK 500 ASP A 377 45.05 -142.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 698 DISTANCE = 6.10 ANGSTROMS 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 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 9 OE1 REMARK 620 2 GLU A 10 OE2 84.5 REMARK 620 3 ASP A 61 OD1 104.5 68.4 REMARK 620 4 GLU A 63 OE1 83.0 148.8 87.3 REMARK 620 5 ASP A 98 OD2 93.1 93.3 152.8 115.8 REMARK 620 N 1 2 3 4 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 9 OE2 REMARK 620 2 GLU A 63 OE2 107.2 REMARK 620 3 ASP A 95 OD1 96.0 80.5 REMARK 620 4 ILE A 96 O 89.0 162.0 90.5 REMARK 620 5 ASP A 98 OD1 92.8 117.4 156.7 68.1 REMARK 620 6 ASP A 131 OD2 158.2 94.1 92.0 70.5 72.8 REMARK 620 N 1 2 3 4 5 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 97 OD1 REMARK 620 2 ASN A 99 O 84.2 REMARK 620 3 ASP A 129 OD1 159.4 75.3 REMARK 620 4 ASP A 129 OD2 142.4 107.4 49.9 REMARK 620 5 ASP A 131 OD1 107.7 74.9 65.2 109.9 REMARK 620 6 ASN A 135 O 100.5 174.6 100.1 67.2 105.9 REMARK 620 7 ASP A 186 OD2 67.6 93.0 115.0 76.0 167.6 86.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 508 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 114 OE1 REMARK 620 2 ASP A 171 OD1 92.5 REMARK 620 3 GLU A 173 OE1 74.1 70.6 REMARK 620 4 ASP A 207 OD2 85.2 164.5 123.1 REMARK 620 N 1 2 3 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 72.8 REMARK 620 3 GLU A 173 OE2 86.8 44.4 REMARK 620 4 ASP A 204 OD1 79.3 113.7 75.7 REMARK 620 5 ALA A 205 O 101.2 146.2 168.3 97.1 REMARK 620 6 ASP A 207 OD1 110.4 85.2 120.1 161.0 65.4 REMARK 620 7 ASP A 240 OD1 164.5 97.1 77.9 94.5 93.7 79.8 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 ASN A 208 O REMARK 620 2 ASP A 238 OD1 76.1 REMARK 620 3 ASP A 238 OD2 93.6 49.6 REMARK 620 4 ASP A 240 OD2 86.4 81.9 129.5 REMARK 620 5 ASN A 244 O 147.3 71.7 69.7 83.8 REMARK 620 6 ASP A 293 OD2 117.0 128.9 79.5 143.4 88.3 REMARK 620 N 1 2 3 4 5 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 223 OE2 REMARK 620 2 GLU A 280 OE1 88.4 REMARK 620 3 GLU A 280 OE2 118.7 45.4 REMARK 620 4 ASP A 309 OD1 76.2 111.6 85.9 REMARK 620 5 GLU A 310 O 72.7 157.3 156.4 76.6 REMARK 620 6 ASP A 312 OD1 88.9 96.6 126.6 147.3 71.1 REMARK 620 7 ASP A 345 OD1 168.7 101.8 72.4 104.0 96.3 85.1 REMARK 620 N 1 2 3 4 5 6 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 223 OE1 REMARK 620 2 ASP A 278 OD1 95.4 REMARK 620 3 GLU A 280 OE1 74.0 90.5 REMARK 620 4 ASP A 312 OD1 92.0 171.4 95.8 REMARK 620 5 ASP A 312 OD2 79.8 132.6 131.4 44.7 REMARK 620 6 HOH A 620 O 82.1 65.4 144.3 111.4 67.2 REMARK 620 N 1 2 3 4 5 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 311 OD1 REMARK 620 2 ASN A 313 O 97.4 REMARK 620 3 ASP A 343 OD1 168.0 72.0 REMARK 620 4 ASP A 343 OD2 137.0 96.3 52.0 REMARK 620 5 ASP A 345 OD2 71.3 77.2 110.6 72.4 REMARK 620 6 ASN A 349 O 92.8 164.4 98.8 68.3 95.0 REMARK 620 7 ASP A 396 OD2 70.6 102.2 105.5 144.2 141.5 92.4 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 6MER A 1 414 UNP Q9Y5G1 PCDGF_HUMAN 31 444 SEQADV 6MER ALA A 415 UNP Q9Y5G1 EXPRESSION TAG SEQADV 6MER 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 *98(H2 O) HELIX 1 AA1 ALA A 21 GLY A 25 5 5 HELIX 2 AA2 GLY A 27 LEU A 31 5 5 HELIX 3 AA3 ASP A 61 CYS A 66 1 6 HELIX 4 AA4 VAL A 132 SER A 136 5 5 HELIX 5 AA5 GLU A 241 ALA A 245 5 5 HELIX 6 AA6 GLY A 255 GLN A 260 1 6 HELIX 7 AA7 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 LEU A 74 O VAL A 91 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 GLY A 18 0 SHEET 2 AA2 3 LEU A 54 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 ILE A 201 N LEU A 110 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 ALA A 222 0 SHEET 2 AA6 4 THR A 298 SER A 308 1 O ASP A 306 N VAL A 219 SHEET 3 AA6 4 SER A 284 LYS A 292 -1 N VAL A 289 O CYS A 301 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 337 HIS A 342 -1 O LEU A 338 N ALA A 320 SHEET 3 AA8 4 THR A 371 THR A 376 -1 O TYR A 372 N ILE A 339 SHEET 4 AA8 4 PHE A 362 GLN A 366 -1 N VAL A 365 O ARG A 373 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 GLN A 355 O THR A 393 SSBOND 1 CYS A 66 CYS A 72 1555 1555 2.03 LINK OE1 GLU A 9 CA CA A 502 1555 1555 2.97 LINK OE2 GLU A 9 CA CA A 503 1555 1555 2.38 LINK OE2 GLU A 10 CA CA A 502 1555 1555 2.58 LINK OD1 ASP A 61 CA CA A 502 1555 1555 2.47 LINK OE1 GLU A 63 CA CA A 502 1555 1555 2.57 LINK OE2 GLU A 63 CA CA A 503 1555 1555 2.43 LINK OD1 ASP A 95 CA CA A 503 1555 1555 2.53 LINK O ILE A 96 CA CA A 503 1555 1555 2.60 LINK OD1 ASN A 97 CA CA A 501 1555 1555 2.46 LINK OD2 ASP A 98 CA CA A 502 1555 1555 2.49 LINK OD1 ASP A 98 CA CA A 503 1555 1555 2.70 LINK O ASN A 99 CA CA A 501 1555 1555 2.60 LINK OE1 GLU A 114 CA CA A 508 1555 1555 2.48 LINK OE2 GLU A 114 CA CA A 509 1555 1555 2.46 LINK OD1 ASP A 129 CA CA A 501 1555 1555 2.57 LINK OD2 ASP A 129 CA CA A 501 1555 1555 2.62 LINK OD1 ASP A 131 CA CA A 501 1555 1555 2.61 LINK OD2 ASP A 131 CA CA A 503 1555 1555 2.38 LINK O ASN A 135 CA CA A 501 1555 1555 2.53 LINK OD1 ASP A 171 CA CA A 508 1555 1555 2.42 LINK OE1 GLU A 173 CA CA A 508 1555 1555 2.50 LINK OE1 GLU A 173 CA CA A 509 1555 1555 3.11 LINK OE2 GLU A 173 CA CA A 509 1555 1555 2.51 LINK OD2 ASP A 186 CA CA A 501 1555 1555 2.63 LINK OD1 ASP A 204 CA CA A 509 1555 1555 2.71 LINK O ALA A 205 CA CA A 509 1555 1555 2.49 LINK OD2 ASP A 207 CA CA A 508 1555 1555 2.45 LINK OD1 ASP A 207 CA CA A 509 1555 1555 2.72 LINK O ASN A 208 CA CA A 507 1555 1555 2.49 LINK OE2 GLU A 223 CA CA A 505 1555 1555 2.45 LINK OE1 GLU A 223 CA CA A 506 1555 1555 2.54 LINK OD1 ASP A 238 CA CA A 507 1555 1555 2.61 LINK OD2 ASP A 238 CA CA A 507 1555 1555 2.62 LINK OD2 ASP A 240 CA CA A 507 1555 1555 2.46 LINK OD1 ASP A 240 CA CA A 509 1555 1555 2.58 LINK O ASN A 244 CA CA A 507 1555 1555 2.52 LINK OD1 ASP A 278 CA CA A 506 1555 1555 2.54 LINK OE1 GLU A 280 CA CA A 505 1555 1555 3.06 LINK OE2 GLU A 280 CA CA A 505 1555 1555 2.42 LINK OE1 GLU A 280 CA CA A 506 1555 1555 2.52 LINK OD2 ASP A 293 CA CA A 507 1555 1555 2.58 LINK OD1 ASP A 309 CA CA A 505 1555 1555 2.57 LINK O GLU A 310 CA CA A 505 1555 1555 2.50 LINK OD1 ASN A 311 CA CA A 504 1555 1555 2.47 LINK OD1 ASP A 312 CA CA A 505 1555 1555 2.50 LINK OD1 ASP A 312 CA CA A 506 1555 1555 3.08 LINK OD2 ASP A 312 CA CA A 506 1555 1555 2.55 LINK O ASN A 313 CA CA A 504 1555 1555 2.44 LINK OD1 ASP A 343 CA CA A 504 1555 1555 2.57 LINK OD2 ASP A 343 CA CA A 504 1555 1555 2.43 LINK OD2 ASP A 345 CA CA A 504 1555 1555 2.62 LINK OD1 ASP A 345 CA CA A 505 1555 1555 2.47 LINK O ASN A 349 CA CA A 504 1555 1555 2.66 LINK OD2 ASP A 396 CA CA A 504 1555 1555 2.52 LINK CA CA A 506 O HOH A 620 1555 1555 2.57 CISPEP 1 LYS A 82 PRO A 83 0 -3.36 CISPEP 2 GLU A 189 PRO A 190 0 -1.02 CISPEP 3 ASN A 399 PRO A 400 0 -0.42 SITE 1 AC1 6 ASN A 97 ASN A 99 ASP A 129 ASP A 131 SITE 2 AC1 6 ASN A 135 ASP A 186 SITE 1 AC2 5 GLU A 9 GLU A 10 ASP A 61 GLU A 63 SITE 2 AC2 5 ASP A 98 SITE 1 AC3 6 GLU A 9 GLU A 63 ASP A 95 ILE A 96 SITE 2 AC3 6 ASP A 98 ASP A 131 SITE 1 AC4 6 ASN A 311 ASN A 313 ASP A 343 ASP A 345 SITE 2 AC4 6 ASN A 349 ASP A 396 SITE 1 AC5 7 GLU A 223 GLU A 280 ASP A 309 GLU A 310 SITE 2 AC5 7 ASP A 312 ASP A 345 CA A 506 SITE 1 AC6 7 GLU A 223 ASP A 278 GLU A 280 ASP A 312 SITE 2 AC6 7 ASN A 313 CA A 505 HOH A 620 SITE 1 AC7 6 ASN A 206 ASN A 208 ASP A 238 ASP A 240 SITE 2 AC7 6 ASN A 244 ASP A 293 SITE 1 AC8 4 GLU A 114 ASP A 171 GLU A 173 ASP A 207 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 128.390 161.770 52.160 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 0.007789 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019172 0.00000