PDB Short entry for 3KUZ HEADER SIGNALING PROTEIN 28-NOV-09 3KUZ TITLE CRYSTAL STRUCTURE OF THE UBIQUITIN LIKE DOMAIN OF PLXNC1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLEXIN-C1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: VIRUS-ENCODED SEMAPHORIN PROTEIN RECEPTOR; 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: PLXNC1, VESPR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL (GI:134105571) KEYWDS PLEXIN, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,B.LI,W.TEMPEL,Y.TONG,X.GUAN,N.ZHONG,L.CROMBET,F.MACKENZIE, AUTHOR 2 M.BUCK,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,J.WEIGELT,A.BOCHKAREV, AUTHOR 3 H.PARK,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 06-SEP-23 3KUZ 1 SEQADV REVDAT 2 01-NOV-17 3KUZ 1 REMARK REVDAT 1 08-DEC-09 3KUZ 0 JRNL AUTH H.WANG,B.LI,W.TEMPEL,Y.TONG,X.GUAN,N.ZHONG,L.CROMBET, JRNL AUTH 2 F.MACKENZIE,M.BUCK,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA, JRNL AUTH 3 J.WEIGELT,A.BOCHKAREV,H.PARK JRNL TITL CRYSTAL STRUCTURE OF THE UBIQUITIN LIKE DOMAIN OF PLXNC1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.251 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.521 REMARK 3 FREE R VALUE TEST SET COUNT : 501 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1006 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.3290 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1603 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.39300 REMARK 3 B22 (A**2) : 1.39300 REMARK 3 B33 (A**2) : -2.78700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.280 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.227 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.178 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1626 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1032 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2204 ; 1.466 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2576 ; 0.843 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 219 ; 5.833 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 61 ;40.394 ;27.377 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 283 ;13.937 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 1 ; 3.823 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 272 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1823 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 278 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1083 ; 0.889 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 451 ; 0.139 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1732 ; 1.695 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 543 ; 2.172 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 471 ; 3.732 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1197 A 1305 4 REMARK 3 1 B 1197 B 1305 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1279 ; 0.220 ; 0.500 REMARK 3 MEDIUM THERMAL 1 B (A**2): 1279 ; 0.490 ; 2.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY. THE PROGRAMS COOT AND REMARK 3 MOLPROBITY WERE ALSO USED DURING REFINEMENT. REMARK 4 REMARK 4 3KUZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056480. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97927 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 : DENZO, HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14277 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.18700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.96300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: SUPERIMPOSED ENSEMBLE OF PDB ENTRIES 3H6N AND 3IG3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 0.2M SODIUM REMARK 280 CHLORIDE, 0.1M HEPES, 1:100 W/W CHYMOTRYPSIN, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 58.11750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.12300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.12300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.17625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.12300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.12300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.05875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.12300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.12300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 87.17625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.12300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.12300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.05875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.11750 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 REMARK: AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS NOT KNOWN. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 MET A 1180 REMARK 465 HIS A 1181 REMARK 465 HIS A 1182 REMARK 465 HIS A 1183 REMARK 465 HIS A 1184 REMARK 465 HIS A 1185 REMARK 465 HIS A 1186 REMARK 465 SER A 1187 REMARK 465 SER A 1188 REMARK 465 GLY A 1189 REMARK 465 ARG A 1190 REMARK 465 GLU A 1191 REMARK 465 ASN A 1192 REMARK 465 LEU A 1193 REMARK 465 TYR A 1194 REMARK 465 PHE A 1195 REMARK 465 MET B 1180 REMARK 465 HIS B 1181 REMARK 465 HIS B 1182 REMARK 465 HIS B 1183 REMARK 465 HIS B 1184 REMARK 465 HIS B 1185 REMARK 465 HIS B 1186 REMARK 465 SER B 1187 REMARK 465 SER B 1188 REMARK 465 GLY B 1189 REMARK 465 ARG B 1190 REMARK 465 GLU B 1191 REMARK 465 ASN B 1192 REMARK 465 LEU B 1193 REMARK 465 TYR B 1194 REMARK 465 PHE B 1195 REMARK 465 GLN B 1196 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A1196 CG CD OE1 NE2 REMARK 470 LYS A1207 CG CD CE NZ REMARK 470 GLU A1212 CG CD OE1 OE2 REMARK 470 SER A1213 OG REMARK 470 ARG A1218 NE CZ NH1 NH2 REMARK 470 GLN A1261 CD OE1 NE2 REMARK 470 THR A1264 OG1 CG2 REMARK 470 ARG A1265 CG CD NE CZ NH1 NH2 REMARK 470 GLN A1266 CG CD OE1 NE2 REMARK 470 GLU A1280 CG CD OE1 OE2 REMARK 470 ASP A1281 CG OD1 OD2 REMARK 470 GLU A1293 OE1 OE2 REMARK 470 LYS A1305 CG CD CE NZ REMARK 470 GLU B1212 CG CD OE1 OE2 REMARK 470 SER B1213 OG REMARK 470 ASP B1215 CG OD1 OD2 REMARK 470 GLN B1261 CG CD OE1 NE2 REMARK 470 THR B1264 OG1 CG2 REMARK 470 ARG B1265 CG CD NE CZ NH1 NH2 REMARK 470 GLN B1266 CG CD OE1 NE2 REMARK 470 GLU B1280 CG CD OE1 OE2 REMARK 470 LYS B1304 CG CD CE NZ REMARK 470 LYS B1305 CG CD CE NZ 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 MET A1262 76.92 -100.27 REMARK 500 GLU B1280 -63.92 -22.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 3KUZ A 1198 1305 UNP O60486 PLXC1_HUMAN 1198 1305 DBREF 3KUZ B 1198 1305 UNP O60486 PLXC1_HUMAN 1198 1305 SEQADV 3KUZ MET A 1180 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS A 1181 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS A 1182 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS A 1183 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS A 1184 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS A 1185 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS A 1186 UNP O60486 EXPRESSION TAG SEQADV 3KUZ SER A 1187 UNP O60486 EXPRESSION TAG SEQADV 3KUZ SER A 1188 UNP O60486 EXPRESSION TAG SEQADV 3KUZ GLY A 1189 UNP O60486 EXPRESSION TAG SEQADV 3KUZ ARG A 1190 UNP O60486 EXPRESSION TAG SEQADV 3KUZ GLU A 1191 UNP O60486 EXPRESSION TAG SEQADV 3KUZ ASN A 1192 UNP O60486 EXPRESSION TAG SEQADV 3KUZ LEU A 1193 UNP O60486 EXPRESSION TAG SEQADV 3KUZ TYR A 1194 UNP O60486 EXPRESSION TAG SEQADV 3KUZ PHE A 1195 UNP O60486 EXPRESSION TAG SEQADV 3KUZ GLN A 1196 UNP O60486 EXPRESSION TAG SEQADV 3KUZ GLY A 1197 UNP O60486 EXPRESSION TAG SEQADV 3KUZ MET B 1180 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS B 1181 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS B 1182 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS B 1183 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS B 1184 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS B 1185 UNP O60486 EXPRESSION TAG SEQADV 3KUZ HIS B 1186 UNP O60486 EXPRESSION TAG SEQADV 3KUZ SER B 1187 UNP O60486 EXPRESSION TAG SEQADV 3KUZ SER B 1188 UNP O60486 EXPRESSION TAG SEQADV 3KUZ GLY B 1189 UNP O60486 EXPRESSION TAG SEQADV 3KUZ ARG B 1190 UNP O60486 EXPRESSION TAG SEQADV 3KUZ GLU B 1191 UNP O60486 EXPRESSION TAG SEQADV 3KUZ ASN B 1192 UNP O60486 EXPRESSION TAG SEQADV 3KUZ LEU B 1193 UNP O60486 EXPRESSION TAG SEQADV 3KUZ TYR B 1194 UNP O60486 EXPRESSION TAG SEQADV 3KUZ PHE B 1195 UNP O60486 EXPRESSION TAG SEQADV 3KUZ GLN B 1196 UNP O60486 EXPRESSION TAG SEQADV 3KUZ GLY B 1197 UNP O60486 EXPRESSION TAG SEQRES 1 A 126 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 126 LEU TYR PHE GLN GLY THR VAL ALA LEU ASN VAL VAL PHE SEQRES 3 A 126 GLU LYS ILE PRO GLU ASN GLU SER ALA ASP VAL CYS ARG SEQRES 4 A 126 ASN ILE SER VAL ASN VAL LEU ASP CYS ASP THR ILE GLY SEQRES 5 A 126 GLN ALA LYS GLU LYS ILE PHE GLN ALA PHE LEU SER LYS SEQRES 6 A 126 ASN GLY SER PRO TYR GLY LEU GLN LEU ASN GLU ILE GLY SEQRES 7 A 126 LEU GLU LEU GLN MET GLY THR ARG GLN LYS GLU LEU LEU SEQRES 8 A 126 ASP ILE ASP SER SER SER VAL ILE LEU GLU ASP GLY ILE SEQRES 9 A 126 THR LYS LEU ASN THR ILE GLY HIS TYR GLU ILE SER ASN SEQRES 10 A 126 GLY SER THR ILE LYS VAL PHE LYS LYS SEQRES 1 B 126 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 B 126 LEU TYR PHE GLN GLY THR VAL ALA LEU ASN VAL VAL PHE SEQRES 3 B 126 GLU LYS ILE PRO GLU ASN GLU SER ALA ASP VAL CYS ARG SEQRES 4 B 126 ASN ILE SER VAL ASN VAL LEU ASP CYS ASP THR ILE GLY SEQRES 5 B 126 GLN ALA LYS GLU LYS ILE PHE GLN ALA PHE LEU SER LYS SEQRES 6 B 126 ASN GLY SER PRO TYR GLY LEU GLN LEU ASN GLU ILE GLY SEQRES 7 B 126 LEU GLU LEU GLN MET GLY THR ARG GLN LYS GLU LEU LEU SEQRES 8 B 126 ASP ILE ASP SER SER SER VAL ILE LEU GLU ASP GLY ILE SEQRES 9 B 126 THR LYS LEU ASN THR ILE GLY HIS TYR GLU ILE SER ASN SEQRES 10 B 126 GLY SER THR ILE LYS VAL PHE LYS LYS HET UNX A 1 1 HET UNX A 2 1 HET UNX A 3 1 HET UNX A 5 1 HET UNX A 7 1 HET UNX A 8 1 HET UNX A 10 1 HET UNX A 11 1 HET UNX B 4 1 HET UNX B 6 1 HET UNX B 9 1 HET UNX B 12 1 HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 UNX 12(X) FORMUL 15 HOH *44(H2 O) HELIX 1 1 THR A 1229 GLY A 1246 1 18 HELIX 2 2 GLN A 1252 ASN A 1254 5 3 HELIX 3 3 ILE A 1289 GLU A 1293 5 5 HELIX 4 4 THR B 1229 GLY B 1246 1 18 HELIX 5 5 GLN B 1252 ASN B 1254 5 3 HELIX 6 6 ILE B 1289 GLU B 1293 5 5 SHEET 1 A 5 ASN A1219 LEU A1225 0 SHEET 2 A 5 THR A1198 PHE A1205 -1 N VAL A1203 O ILE A1220 SHEET 3 A 5 THR A1299 LYS A1304 1 O VAL A1302 N VAL A1204 SHEET 4 A 5 ILE A1256 MET A1262 -1 N GLU A1259 O LYS A1301 SHEET 5 A 5 ARG A1265 LEU A1269 -1 O LYS A1267 N LEU A1260 SHEET 1 B 5 ASN B1219 LEU B1225 0 SHEET 2 B 5 THR B1198 PHE B1205 -1 N LEU B1201 O VAL B1222 SHEET 3 B 5 THR B1299 LYS B1304 1 O VAL B1302 N VAL B1204 SHEET 4 B 5 ILE B1256 MET B1262 -1 N GLU B1259 O LYS B1301 SHEET 5 B 5 ARG B1265 LEU B1269 -1 O LYS B1267 N LEU B1260 SSBOND 1 CYS A 1227 CYS B 1227 1555 1555 2.09 CRYST1 72.246 72.246 116.235 90.00 90.00 90.00 P 43 21 2 16 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 0.013842 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013842 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008603 0.00000