HEADER MEMBRANE PROTEIN/PROTEIN BINDING 21-DEC-10 3Q3J TITLE CRYSTAL STRUCTURE OF PLEXIN A2 RBD IN COMPLEX WITH RND1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLEXIN-A2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1490-1600; COMPND 5 SYNONYM: SEMAPHORIN RECEPTOR OCT; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RHO-RELATED GTP-BINDING PROTEIN RHO6; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 5-200; COMPND 11 SYNONYM: RHO FAMILY GTPASE 1, RND1; COMPND 12 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: PLXNA2, KIAA0463, OCT, PLXN2, UNQ209/PRO235; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL (GI:134105571); SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: RND1, RHO6; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET28-MHL (GI:134105571) KEYWDS RAS-BINDING DOMAIN, PLEXIN, SMALL GTPASE, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, MEMBRANE PROTEIN-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,W.TEMPEL,Y.TONG,X.GUAN,L.SHEN,L.BUREN,N.ZHANG,A.K.WERNIMONT, AUTHOR 2 L.CROMBET,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,J.WEIGELT,H.PARK, AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 13-SEP-23 3Q3J 1 REMARK SEQADV LINK REVDAT 2 08-NOV-17 3Q3J 1 REMARK REVDAT 1 12-JAN-11 3Q3J 0 JRNL AUTH H.WANG,W.TEMPEL,Y.TONG,X.GUAN,L.SHEN,L.BUREN,N.ZHANG, JRNL AUTH 2 A.K.WERNIMONT,L.CROMBET,C.H.ARROWSMITH,A.M.EDWARDS, JRNL AUTH 3 C.BOUNTRA,J.WEIGELT,H.PARK JRNL TITL CRYSTAL STRUCTURE OF PLEXIN A2 RBD IN COMPLEX WITH RND1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 20667 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.187 REMARK 3 FREE R VALUE TEST SET COUNT : 1072 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) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1367 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2065 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 38 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.59500 REMARK 3 B22 (A**2) : 0.24100 REMARK 3 B33 (A**2) : 0.35400 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.165 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.979 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2140 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1352 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2927 ; 1.195 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3338 ; 0.873 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 5.593 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;36.949 ;24.595 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 340 ;12.195 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.304 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 360 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2331 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 387 ; 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): 1390 ; 0.491 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 550 ; 0.118 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2239 ; 0.938 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 750 ; 1.512 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 688 ; 2.383 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -7.5439 12.2882 31.4727 REMARK 3 T TENSOR REMARK 3 T11: 0.1051 T22: 0.1056 REMARK 3 T33: 0.1367 T12: -0.0076 REMARK 3 T13: 0.0102 T23: 0.0306 REMARK 3 L TENSOR REMARK 3 L11: 6.5009 L22: 3.7863 REMARK 3 L33: 4.9229 L12: 0.6347 REMARK 3 L13: -1.6201 L23: 0.8977 REMARK 3 S TENSOR REMARK 3 S11: -0.0772 S12: 0.2227 S13: -0.0837 REMARK 3 S21: -0.1597 S22: -0.2215 S23: 0.3366 REMARK 3 S31: 0.0296 S32: -0.4443 S33: 0.2987 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 14.6512 22.6165 14.0516 REMARK 3 T TENSOR REMARK 3 T11: 0.1158 T22: 0.0992 REMARK 3 T33: 0.0217 T12: -0.0499 REMARK 3 T13: -0.0226 T23: 0.0340 REMARK 3 L TENSOR REMARK 3 L11: 3.4037 L22: 2.5825 REMARK 3 L33: 2.0134 L12: 1.3583 REMARK 3 L13: -0.5128 L23: -0.6195 REMARK 3 S TENSOR REMARK 3 S11: -0.1414 S12: 0.3181 S13: -0.0140 REMARK 3 S21: -0.2292 S22: 0.2146 S23: 0.1209 REMARK 3 S31: 0.0824 S32: -0.1360 S33: -0.0732 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REMARK 3 WITH TLS ADDED. REMARK 3 REMARK 3 THE PROGRAMS CHAINSAW (CCP4) AND COOT AND THE MOLPROBITY SERVER REMARK 3 WERE ALSO USED DURING REFINEMENT. REMARK 4 REMARK 4 3Q3J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000063148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-10 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) : 0.98322 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 : 20734 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.96400 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRIES 2REX, 3IG3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE COMPLEX SAMPLE (2.7 MG/ML) WAS REMARK 280 INCUBATED WITH 5MM GPP(NH)P. CRYSTALLIZATION COCKTAIL: 25.5% REMARK 280 PEG3350, 0.2 M MAGNESIUM CHLORIDE, 0.1M HEPES. SEEDING WAS REMARK 280 APPLIED IN THE PRODUCTION OF THE DIFFRACTION-QUALITY CRYSTAL., REMARK 280 PH 7.5, VAPOR DIFFUSION, SITTING DROPS, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 0.00000 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 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 1.000000 0.000000 0.000000 29.51100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.56450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.64550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.51100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.56450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.64550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.51100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.56450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.64550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.51100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.56450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.64550 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 51980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -138.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 67.12900 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 67.12900 REMARK 350 BIOMT3 4 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 UNK UNX B 203 LIES ON A SPECIAL POSITION. REMARK 375 UNK UNX B 204 LIES ON A SPECIAL POSITION. 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 GLY A 1489 REMARK 465 ASN A 1539 REMARK 465 VAL A 1540 REMARK 465 PRO A 1541 REMARK 465 TYR A 1542 REMARK 465 SER A 1543 REMARK 465 GLU A 1575 REMARK 465 GLY A 1576 REMARK 465 ASP A 1577 REMARK 465 TRP A 1578 REMARK 465 MET B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 SER B -6 REMARK 465 SER B -5 REMARK 465 GLY B -4 REMARK 465 ARG B -3 REMARK 465 GLU B -2 REMARK 465 ASN B -1 REMARK 465 LEU B 0 REMARK 465 TYR B 1 REMARK 465 PHE B 2 REMARK 465 GLN B 3 REMARK 465 GLY B 4 REMARK 465 ARG B 5 REMARK 465 ALA B 6 REMARK 465 PRO B 7 REMARK 465 GLN B 8 REMARK 465 PRO B 9 REMARK 465 VAL B 10 REMARK 465 VAL B 11 REMARK 465 ALA B 12 REMARK 465 GLU B 57 REMARK 465 GLU B 58 REMARK 465 LYS B 190 REMARK 465 PRO B 191 REMARK 465 SER B 192 REMARK 465 PRO B 193 REMARK 465 LEU B 194 REMARK 465 PRO B 195 REMARK 465 GLN B 196 REMARK 465 LYS B 197 REMARK 465 SER B 198 REMARK 465 PRO B 199 REMARK 465 VAL B 200 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 GLU A1496 CG CD OE1 OE2 REMARK 470 LYS A1498 CE NZ REMARK 470 ASN A1509 CG OD1 ND2 REMARK 470 GLU A1510 CG CD OE1 OE2 REMARK 470 ASN A1511 CG OD1 ND2 REMARK 470 SER A1512 OG REMARK 470 GLU A1514 OE1 OE2 REMARK 470 LYS A1518 CE NZ REMARK 470 LYS A1538 CD CE NZ REMARK 470 GLN A1544 CG CD OE1 NE2 REMARK 470 ARG A1545 NE CZ NH1 NH2 REMARK 470 ARG A1559 CG CD NE CZ NH1 NH2 REMARK 470 ILE A1560 CG1 CG2 CD1 REMARK 470 GLU A1568 CD OE1 OE2 REMARK 470 LYS A1573 CG CD CE NZ REMARK 470 LYS A1579 CG CD CE NZ REMARK 470 ARG A1580 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1592 CD NE CZ NH1 NH2 REMARK 470 ARG B 13 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 31 OE1 NE2 REMARK 470 LYS B 35 CD CE NZ REMARK 470 GLU B 40 CG CD OE1 OE2 REMARK 470 THR B 41 OG1 CG2 REMARK 470 VAL B 43 CG1 CG2 REMARK 470 GLU B 55 CG CD OE1 OE2 REMARK 470 THR B 56 OG1 CG2 REMARK 470 ARG B 60 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 62 CG CD OE1 OE2 REMARK 470 LEU B 133 CG CD1 CD2 REMARK 470 GLU B 138 CD OE1 OE2 REMARK 470 LYS B 143 CE NZ REMARK 470 LYS B 157 CG CD CE NZ REMARK 470 GLN B 158 CG CD OE1 NE2 REMARK 470 GLU B 162 CD OE1 OE2 REMARK 470 GLU B 173 CG CD OE1 OE2 REMARK 470 LYS B 174 CD CE NZ REMARK 470 ARG B 181 NE CZ NH1 NH2 REMARK 470 MET B 185 CG SD CE REMARK 470 LEU B 188 CG CD1 CD2 REMARK 470 ASN B 189 CG OD1 ND2 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 ASP A1569 -167.88 -161.51 REMARK 500 GLN B 23 17.41 56.47 REMARK 500 VAL B 46 -77.58 -98.82 REMARK 500 LYS B 105 -86.53 -111.32 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 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 27 OG1 REMARK 620 2 THR B 45 OG1 84.6 REMARK 620 3 HOH B 224 O 86.4 89.1 REMARK 620 4 HOH B 225 O 86.7 93.6 172.4 REMARK 620 5 GNP B 500 O2G 177.8 94.3 95.4 91.5 REMARK 620 6 GNP B 500 O1B 88.9 173.4 89.4 87.0 92.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 201 DBREF 3Q3J A 1490 1600 UNP O75051 PLXA2_HUMAN 1490 1600 DBREF 3Q3J B 5 200 UNP Q92730 RND1_HUMAN 5 200 SEQADV 3Q3J GLY A 1489 UNP O75051 EXPRESSION TAG SEQADV 3Q3J MET B -13 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J HIS B -12 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J HIS B -11 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J HIS B -10 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J HIS B -9 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J HIS B -8 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J HIS B -7 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J SER B -6 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J SER B -5 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J GLY B -4 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J ARG B -3 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J GLU B -2 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J ASN B -1 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J LEU B 0 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J TYR B 1 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J PHE B 2 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J GLN B 3 UNP Q92730 EXPRESSION TAG SEQADV 3Q3J GLY B 4 UNP Q92730 EXPRESSION TAG SEQRES 1 A 112 GLY LEU ILE ARG GLN GLN ILE GLU TYR LYS THR LEU ILE SEQRES 2 A 112 LEU ASN CYS VAL ASN PRO ASP ASN GLU ASN SER PRO GLU SEQRES 3 A 112 ILE PRO VAL LYS VAL LEU ASN CYS ASP THR ILE THR GLN SEQRES 4 A 112 VAL LYS GLU LYS ILE LEU ASP ALA VAL TYR LYS ASN VAL SEQRES 5 A 112 PRO TYR SER GLN ARG PRO ARG ALA VAL ASP MET ASP LEU SEQRES 6 A 112 GLU TRP ARG GLN GLY ARG ILE ALA ARG VAL VAL LEU GLN SEQRES 7 A 112 ASP GLU ASP ILE THR THR LYS ILE GLU GLY ASP TRP LYS SEQRES 8 A 112 ARG LEU ASN THR LEU MET HIS TYR GLN VAL SER ASP ARG SEQRES 9 A 112 SER VAL VAL ALA LEU VAL PRO LYS SEQRES 1 B 214 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 B 214 LEU TYR PHE GLN GLY ARG ALA PRO GLN PRO VAL VAL ALA SEQRES 3 B 214 ARG CYS LYS LEU VAL LEU VAL GLY ASP VAL GLN CYS GLY SEQRES 4 B 214 LYS THR ALA MET LEU GLN VAL LEU ALA LYS ASP CYS TYR SEQRES 5 B 214 PRO GLU THR TYR VAL PRO THR VAL PHE GLU ASN TYR THR SEQRES 6 B 214 ALA CYS LEU GLU THR GLU GLU GLN ARG VAL GLU LEU SER SEQRES 7 B 214 LEU TRP ASP THR SER GLY SER PRO TYR TYR ASP ASN VAL SEQRES 8 B 214 ARG PRO LEU CYS TYR SER ASP SER ASP ALA VAL LEU LEU SEQRES 9 B 214 CYS PHE ASP ILE SER ARG PRO GLU THR VAL ASP SER ALA SEQRES 10 B 214 LEU LYS LYS TRP ARG THR GLU ILE LEU ASP TYR CYS PRO SEQRES 11 B 214 SER THR ARG VAL LEU LEU ILE GLY CYS LYS THR ASP LEU SEQRES 12 B 214 ARG THR ASP LEU SER THR LEU MET GLU LEU SER HIS GLN SEQRES 13 B 214 LYS GLN ALA PRO ILE SER TYR GLU GLN GLY CYS ALA ILE SEQRES 14 B 214 ALA LYS GLN LEU GLY ALA GLU ILE TYR LEU GLU GLY SER SEQRES 15 B 214 ALA PHE THR SER GLU LYS SER ILE HIS SER ILE PHE ARG SEQRES 16 B 214 THR ALA SER MET LEU CYS LEU ASN LYS PRO SER PRO LEU SEQRES 17 B 214 PRO GLN LYS SER PRO VAL HET UNX A 1 1 HET UNX A 6 1 HET GNP B 500 32 HET MG B 201 1 HET UNX B 202 1 HET UNX B 203 1 HET UNX B 204 1 HET UNX B 205 1 HET UNX B 206 1 HET UNX B 207 1 HET UNX B 208 1 HETNAM UNX UNKNOWN ATOM OR ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 3 UNX 9(X) FORMUL 5 GNP C10 H17 N6 O13 P3 FORMUL 6 MG MG 2+ FORMUL 14 HOH *38(H2 O) HELIX 1 1 THR A 1524 TYR A 1537 1 14 HELIX 2 2 ARG A 1547 VAL A 1549 5 3 HELIX 3 3 THR A 1583 GLN A 1588 1 6 HELIX 4 4 GLY B 25 ASP B 36 1 12 HELIX 5 5 SER B 71 ASP B 75 5 5 HELIX 6 6 VAL B 77 TYR B 82 5 6 HELIX 7 7 PRO B 97 LYS B 105 1 9 HELIX 8 8 LYS B 105 CYS B 115 1 11 HELIX 9 9 LYS B 126 THR B 131 5 6 HELIX 10 10 ASP B 132 GLN B 142 1 11 HELIX 11 11 SER B 148 GLY B 160 1 13 HELIX 12 12 SER B 172 ASN B 189 1 18 SHEET 1 A 5 ILE A1515 LEU A1520 0 SHEET 2 A 5 THR A1499 CYS A1504 -1 N CYS A1504 O ILE A1515 SHEET 3 A 5 VAL A1594 PRO A1599 1 O VAL A1595 N ASN A1503 SHEET 4 A 5 MET A1551 GLN A1557 -1 N GLU A1554 O ALA A1596 SHEET 5 A 5 ALA A1561 LEU A1565 -1 O VAL A1563 N TRP A1555 SHEET 1 B 6 PHE B 47 LEU B 54 0 SHEET 2 B 6 VAL B 61 THR B 68 -1 O LEU B 63 N ALA B 52 SHEET 3 B 6 CYS B 14 VAL B 19 1 N LEU B 18 O TRP B 66 SHEET 4 B 6 ALA B 87 ASP B 93 1 O CYS B 91 N VAL B 19 SHEET 5 B 6 ARG B 119 CYS B 125 1 O ILE B 123 N LEU B 90 SHEET 6 B 6 ILE B 163 GLU B 166 1 O LEU B 165 N LEU B 122 LINK OG1 THR B 27 MG MG B 201 1555 1555 2.00 LINK OG1 THR B 45 MG MG B 201 1555 1555 2.05 LINK MG MG B 201 O HOH B 224 1555 1555 2.22 LINK MG MG B 201 O HOH B 225 1555 1555 2.10 LINK MG MG B 201 O2G GNP B 500 1555 1555 1.96 LINK MG MG B 201 O1B GNP B 500 1555 1555 2.00 SITE 1 AC1 26 VAL B 22 GLN B 23 CYS B 24 GLY B 25 SITE 2 AC1 26 LYS B 26 THR B 27 ALA B 28 TYR B 38 SITE 3 AC1 26 PRO B 39 GLU B 40 THR B 41 TYR B 42 SITE 4 AC1 26 THR B 45 GLY B 70 LYS B 126 ASP B 128 SITE 5 AC1 26 LEU B 129 SER B 168 ALA B 169 PHE B 170 SITE 6 AC1 26 MG B 201 HOH B 218 HOH B 224 HOH B 225 SITE 7 AC1 26 HOH B 228 HOH B 232 SITE 1 AC2 5 THR B 27 THR B 45 HOH B 224 HOH B 225 SITE 2 AC2 5 GNP B 500 CRYST1 59.022 67.129 145.291 90.00 90.00 90.00 I 2 2 2 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 0.016943 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014897 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006883 0.00000