HEADER SIGNALING PROTEIN 02-OCT-12 4HDQ TITLE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF KRIT1 BOUND TO BOTH THE TITLE 2 RAP1 GTPASE AND THE HEART OF GLASS (HEG1) CYTOPLASMIC TAIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: KREV INTERACTION TRAPPED PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FERM DOMAIN (UNP RESIDUES 417-736); COMPND 5 SYNONYM: KRIT1, KREV INTERACTION TRAPPED 1, CEREBRAL CAVERNOUS COMPND 6 MALFORMATIONS 1 PROTEIN; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RAS-RELATED PROTEIN RAP-1B; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 1-167; COMPND 12 SYNONYM: RAP1B, GTP-BINDING PROTEIN SMG P21B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: PROTEIN HEG HOMOLOG 1; COMPND 16 CHAIN: C; COMPND 17 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 1356-1381); COMPND 18 SYNONYM: HEG1; COMPND 19 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: KRIT1, CCM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 STAR (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLEICS-07; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RAP1B, OK/SW-CL.11; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21 STAR (DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PTAC; SOURCE 21 MOL_ID: 3; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606 KEYWDS RA BINDING MOTIF, GTPASE, HEG1 CYTOPLASMIC TAIL, PTD DOMAIN, RAP1 KEYWDS 2 EFFECTOR, TRANSMEMBRANE PROTEIN, RAP1, HEG1, CELL-CELL JUNCTIONS, KEYWDS 3 PLASMA MEMBRANE, NUCLEUS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.R.GINGRAS REVDAT 4 20-SEP-23 4HDQ 1 REMARK SEQADV LINK REVDAT 3 04-SEP-13 4HDQ 1 JRNL REVDAT 2 17-JUL-13 4HDQ 1 JRNL REVDAT 1 10-JUL-13 4HDQ 0 JRNL AUTH A.R.GINGRAS,W.PUZON-MCLAUGHLIN,M.H.GINSBERG JRNL TITL THE STRUCTURE OF THE TERNARY COMPLEX OF KREV INTERACTION JRNL TITL 2 TRAPPED 1 (KRIT1) BOUND TO BOTH THE RAP1 GTPASE AND THE JRNL TITL 3 HEART OF GLASS (HEG1) CYTOPLASMIC TAIL. JRNL REF J.BIOL.CHEM. V. 288 23639 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23814056 JRNL DOI 10.1074/JBC.M113.462911 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 35112 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1848 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2398 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3877 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.40000 REMARK 3 B22 (A**2) : 1.27000 REMARK 3 B33 (A**2) : 0.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.97000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.183 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.177 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.124 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.330 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3996 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2721 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5401 ; 1.932 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6657 ; 1.038 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 478 ; 7.455 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 189 ;41.752 ;24.815 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 740 ;17.137 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;20.053 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 603 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4343 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 786 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4HDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36963 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.34700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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: PDB ENTRY 4HDO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG2000 MME, 100 MM TRIS, 100 MM REMARK 280 POTASSIUM CHLORIDE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 38.70500 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A 415 REMARK 465 ALA A 416 REMARK 465 LYS A 417 REMARK 465 PRO A 418 REMARK 465 MET A 730 REMARK 465 PRO A 731 REMARK 465 THR A 732 REMARK 465 GLU A 733 REMARK 465 ARG A 734 REMARK 465 ASN A 735 REMARK 465 SER A 736 REMARK 465 GLN B 63 REMARK 465 PHE B 64 REMARK 465 THR B 65 REMARK 465 SER C 1356 REMARK 465 ARG C 1357 REMARK 465 HIS C 1358 REMARK 465 SER C 1359 REMARK 465 CYS C 1360 REMARK 465 ILE C 1361 REMARK 465 PHE C 1362 REMARK 465 PRO C 1363 REMARK 465 GLY C 1364 REMARK 465 GLN C 1365 REMARK 465 TYR C 1366 REMARK 465 ASN C 1367 REMARK 465 PRO C 1368 REMARK 465 SER C 1369 REMARK 465 PHE C 1370 REMARK 465 ILE C 1371 REMARK 465 SER C 1372 REMARK 465 ASP C 1373 REMARK 465 GLU C 1374 REMARK 465 SER C 1375 REMARK 465 ARG C 1376 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 SER A 651 OG REMARK 470 ASN A 652 CG OD1 ND2 REMARK 470 HIS A 653 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 62 CG CD OE1 OE2 REMARK 470 ARG C1377 CG CD NE CZ NH1 NH2 REMARK 470 ARG C1378 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 478 CG HIS A 478 CD2 0.077 REMARK 500 HIS A 596 CG HIS A 596 CD2 0.057 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 510 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 511 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP A 548 CB - CG - OD1 ANGL. DEV. = 8.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 440 0.02 -64.93 REMARK 500 SER A 467 -167.29 -112.68 REMARK 500 GLU A 578 -70.52 -56.56 REMARK 500 PRO A 595 -32.82 -37.43 REMARK 500 LYS A 647 72.00 -107.73 REMARK 500 ALA A 648 -57.88 -127.32 REMARK 500 SER A 649 -112.20 158.54 REMARK 500 PRO A 650 105.54 23.00 REMARK 500 SER A 651 -101.82 88.27 REMARK 500 ASN A 652 47.80 -178.70 REMARK 500 HIS A 653 -106.69 -149.03 REMARK 500 LYS A 675 17.30 59.86 REMARK 500 GLU A 703 45.68 98.97 REMARK 500 ASN A 704 -21.29 148.34 REMARK 500 LYS A 705 62.74 21.35 REMARK 500 THR A 712 139.63 -172.24 REMARK 500 ASP B 33 89.52 -159.55 REMARK 500 ILE B 36 -61.77 -90.27 REMARK 500 GLU B 37 109.75 -171.43 REMARK 500 LEU B 120 55.42 -97.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 452 LEU A 453 -149.10 REMARK 500 ALA A 648 SER A 649 144.81 REMARK 500 SER A 651 ASN A 652 144.16 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 200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 17 OG REMARK 620 2 THR B 35 OG1 88.0 REMARK 620 3 GNP B 201 O1B 94.1 174.7 REMARK 620 4 GNP B 201 O1G 167.7 80.1 97.9 REMARK 620 5 HOH B 301 O 92.8 90.2 94.5 84.0 REMARK 620 6 HOH B 302 O 84.7 83.5 91.9 97.2 173.3 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 GOL A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HDO RELATED DB: PDB REMARK 900 KRIT1 FERM DOMAIN + RAP1B DBREF 4HDQ A 417 736 UNP O00522 KRIT1_HUMAN 417 736 DBREF 4HDQ B 1 167 UNP P61224 RAP1B_HUMAN 1 167 DBREF 4HDQ C 1356 1381 UNP Q9ULI3 HEG1_HUMAN 1356 1381 SEQADV 4HDQ GLY A 415 UNP O00522 EXPRESSION TAG SEQADV 4HDQ ALA A 416 UNP O00522 EXPRESSION TAG SEQRES 1 A 322 GLY ALA LYS PRO TYR GLU LYS VAL ARG ILE TYR ARG MET SEQRES 2 A 322 ASP GLY SER TYR ARG SER VAL GLU LEU LYS HIS GLY ASN SEQRES 3 A 322 ASN THR THR VAL GLN GLN ILE MET GLU GLY MET ARG LEU SEQRES 4 A 322 SER GLN GLU THR GLN GLN TYR PHE THR ILE TRP ILE CYS SEQRES 5 A 322 SER GLU ASN LEU SER LEU GLN LEU LYS PRO TYR HIS LYS SEQRES 6 A 322 PRO LEU GLN HIS VAL ARG ASP TRP PRO GLU ILE LEU ALA SEQRES 7 A 322 GLU LEU THR ASN LEU ASP PRO GLN ARG GLU THR PRO GLN SEQRES 8 A 322 LEU PHE LEU ARG ARG ASP VAL ARG LEU PRO LEU GLU VAL SEQRES 9 A 322 GLU LYS GLN ILE GLU ASP PRO LEU ALA ILE LEU ILE LEU SEQRES 10 A 322 PHE ASP GLU ALA ARG TYR ASN LEU LEU LYS GLY PHE TYR SEQRES 11 A 322 THR ALA PRO ASP ALA LYS LEU ILE THR LEU ALA SER LEU SEQRES 12 A 322 LEU LEU GLN ILE VAL TYR GLY ASN TYR GLU SER LYS LYS SEQRES 13 A 322 HIS LYS GLN GLY PHE LEU ASN GLU GLU ASN LEU LYS SER SEQRES 14 A 322 ILE VAL PRO VAL THR LYS LEU LYS SER LYS ALA PRO HIS SEQRES 15 A 322 TRP THR ASN ARG ILE LEU HIS GLU TYR LYS ASN LEU SER SEQRES 16 A 322 THR SER GLU GLY VAL SER LYS GLU MET HIS HIS LEU GLN SEQRES 17 A 322 ARG MET PHE LEU GLN ASN CYS TRP GLU ILE PRO THR TYR SEQRES 18 A 322 GLY ALA ALA PHE PHE THR GLY GLN ILE PHE THR LYS ALA SEQRES 19 A 322 SER PRO SER ASN HIS LYS VAL ILE PRO VAL TYR VAL GLY SEQRES 20 A 322 VAL ASN ILE LYS GLY LEU HIS LEU LEU ASN MET GLU THR SEQRES 21 A 322 LYS ALA LEU LEU ILE SER LEU LYS TYR GLY CYS PHE MET SEQRES 22 A 322 TRP GLN LEU GLY ASP THR ASP THR CYS PHE GLN ILE HIS SEQRES 23 A 322 SER MET GLU ASN LYS MET SER PHE ILE VAL HIS THR LYS SEQRES 24 A 322 GLN ALA GLY LEU VAL VAL LYS LEU LEU MET LYS LEU ASN SEQRES 25 A 322 GLY GLN LEU MET PRO THR GLU ARG ASN SER SEQRES 1 B 167 MET ARG GLU TYR LYS LEU VAL VAL LEU GLY SER GLY GLY SEQRES 2 B 167 VAL GLY LYS SER ALA LEU THR VAL GLN PHE VAL GLN GLY SEQRES 3 B 167 ILE PHE VAL GLU LYS TYR ASP PRO THR ILE GLU ASP SER SEQRES 4 B 167 TYR ARG LYS GLN VAL GLU VAL ASP ALA GLN GLN CYS MET SEQRES 5 B 167 LEU GLU ILE LEU ASP THR ALA GLY THR GLU GLN PHE THR SEQRES 6 B 167 ALA MET ARG ASP LEU TYR MET LYS ASN GLY GLN GLY PHE SEQRES 7 B 167 ALA LEU VAL TYR SER ILE THR ALA GLN SER THR PHE ASN SEQRES 8 B 167 ASP LEU GLN ASP LEU ARG GLU GLN ILE LEU ARG VAL LYS SEQRES 9 B 167 ASP THR ASP ASP VAL PRO MET ILE LEU VAL GLY ASN LYS SEQRES 10 B 167 CYS ASP LEU GLU ASP GLU ARG VAL VAL GLY LYS GLU GLN SEQRES 11 B 167 GLY GLN ASN LEU ALA ARG GLN TRP ASN ASN CYS ALA PHE SEQRES 12 B 167 LEU GLU SER SER ALA LYS SER LYS ILE ASN VAL ASN GLU SEQRES 13 B 167 ILE PHE TYR ASP LEU VAL ARG GLN ILE ASN ARG SEQRES 1 C 26 SER ARG HIS SER CYS ILE PHE PRO GLY GLN TYR ASN PRO SEQRES 2 C 26 SER PHE ILE SER ASP GLU SER ARG ARG ARG ASP TYR PHE HET GOL A 801 6 HET MG B 200 1 HET GNP B 201 32 HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL C3 H8 O3 FORMUL 5 MG MG 2+ FORMUL 6 GNP C10 H17 N6 O13 P3 FORMUL 7 HOH *93(H2 O) HELIX 1 1 HIS A 438 THR A 442 5 5 HELIX 2 2 THR A 443 GLY A 450 1 8 HELIX 3 3 SER A 454 GLN A 459 1 6 HELIX 4 4 LYS A 479 ASP A 486 1 8 HELIX 5 5 ASP A 486 THR A 495 1 10 HELIX 6 6 ASP A 498 GLU A 502 5 5 HELIX 7 7 PRO A 515 LYS A 520 1 6 HELIX 8 8 ASP A 524 LYS A 541 1 18 HELIX 9 9 PRO A 547 GLY A 564 1 18 HELIX 10 10 GLU A 567 LYS A 572 1 6 HELIX 11 11 ASN A 577 LYS A 582 1 6 HELIX 12 12 PRO A 586 LEU A 590 5 5 HELIX 13 13 LYS A 593 HIS A 596 5 4 HELIX 14 14 TRP A 597 SER A 611 1 15 HELIX 15 15 GLU A 617 GLU A 631 1 15 HELIX 16 16 GLN A 714 LEU A 729 1 16 HELIX 17 17 GLY B 15 GLY B 26 1 12 HELIX 18 18 MET B 67 GLY B 75 1 9 HELIX 19 19 ALA B 86 ASP B 92 1 7 HELIX 20 20 ASP B 92 ASP B 105 1 14 HELIX 21 21 LEU B 120 ARG B 124 5 5 HELIX 22 22 GLY B 127 TRP B 138 1 12 HELIX 23 23 ASN B 153 ARG B 167 1 15 SHEET 1 A11 SER A 471 GLN A 473 0 SHEET 2 A11 PHE A 461 CYS A 466 -1 N ILE A 465 O LEU A 472 SHEET 3 A11 GLN A 505 ARG A 510 -1 O PHE A 507 N TRP A 464 SHEET 4 A11 GLU A 420 TYR A 425 1 N TYR A 425 O LEU A 506 SHEET 5 A11 TYR A 431 LEU A 436 -1 O ARG A 432 N ILE A 424 SHEET 6 A11 GLU B 37 VAL B 46 -1 O SER B 39 N TYR A 431 SHEET 7 A11 GLN B 49 THR B 58 -1 O GLN B 49 N VAL B 46 SHEET 8 A11 GLU B 3 LEU B 9 1 N LEU B 6 O GLU B 54 SHEET 9 A11 GLY B 77 SER B 83 1 O ALA B 79 N LEU B 9 SHEET 10 A11 MET B 111 ASN B 116 1 O ILE B 112 N LEU B 80 SHEET 11 A11 ALA B 142 GLU B 145 1 O LEU B 144 N GLY B 115 SHEET 1 B 4 ALA A 638 PHE A 645 0 SHEET 2 B 4 VAL A 655 VAL A 662 -1 O ILE A 656 N ILE A 644 SHEET 3 B 4 GLY A 666 ASN A 671 -1 O HIS A 668 N GLY A 661 SHEET 4 B 4 LEU A 677 LYS A 682 -1 O ILE A 679 N LEU A 669 SHEET 1 C 3 MET A 687 LEU A 690 0 SHEET 2 C 3 CYS A 696 SER A 701 -1 O GLN A 698 N GLN A 689 SHEET 3 C 3 MET A 706 HIS A 711 -1 O MET A 706 N SER A 701 LINK OG SER B 17 MG MG B 200 1555 1555 2.13 LINK OG1 THR B 35 MG MG B 200 1555 1555 2.13 LINK MG MG B 200 O1B GNP B 201 1555 1555 1.98 LINK MG MG B 200 O1G GNP B 201 1555 1555 2.08 LINK MG MG B 200 O HOH B 301 1555 1555 2.18 LINK MG MG B 200 O HOH B 302 1555 1555 1.91 CISPEP 1 ASN A 652 HIS A 653 0 21.12 SITE 1 AC1 4 ASN A 469 LEU A 470 SER A 471 PHE A 639 SITE 1 AC2 5 SER B 17 THR B 35 GNP B 201 HOH B 301 SITE 2 AC2 5 HOH B 302 SITE 1 AC3 23 GLY B 13 VAL B 14 GLY B 15 LYS B 16 SITE 2 AC3 23 SER B 17 ALA B 18 PHE B 28 VAL B 29 SITE 3 AC3 23 GLU B 30 PRO B 34 THR B 35 GLY B 60 SITE 4 AC3 23 ASN B 116 LYS B 117 ASP B 119 LEU B 120 SITE 5 AC3 23 SER B 147 ALA B 148 LYS B 149 MG B 200 SITE 6 AC3 23 HOH B 301 HOH B 302 HOH B 320 CRYST1 57.310 77.410 58.570 90.00 95.56 90.00 P 1 21 1 2 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 0.017449 0.000000 0.001700 0.00000 SCALE2 0.000000 0.012918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017154 0.00000