HEADER HYDROLASE 11-APR-19 6JTG TITLE STRUCTURAL INSIGHTS INTO G DOMAIN DIMERIZATION AND PATHOGENIC TITLE 2 MUTATIONS OF OPA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DYNAMIN-LIKE 120 KDA PROTEIN, MITOCHONDRIAL,OPA1 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 267-318,UNP RESIDUES 254-276; COMPND 5 SYNONYM: OPTIC ATROPHY PROTEIN 1; COMPND 6 EC: 3.6.5.5; COMPND 7 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: OPA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MITOCHONDRIA, FUSION, OPA1, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.YAN,J.HU REVDAT 3 27-MAR-24 6JTG 1 LINK REVDAT 2 20-MAY-20 6JTG 1 JRNL REVDAT 1 22-APR-20 6JTG 0 JRNL AUTH C.YU,J.ZHAO,L.YAN,Y.QI,X.GUO,Z.LOU,J.HU,Z.RAO JRNL TITL STRUCTURAL INSIGHTS INTO G DOMAIN DIMERIZATION AND JRNL TITL 2 PATHOGENIC MUTATION OF OPA1. JRNL REF J.CELL BIOL. V. 219 2020 JRNL REFN ESSN 1540-8140 JRNL PMID 32379273 JRNL DOI 10.1083/JCB.201907098 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 NUMBER OF REFLECTIONS : 21509 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3544 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 46.3535 - 7.0058 1.00 1419 157 0.1824 0.2027 REMARK 3 2 7.0058 - 5.5637 1.00 1428 153 0.1995 0.2452 REMARK 3 3 5.5637 - 4.8613 1.00 1419 161 0.1794 0.2039 REMARK 3 4 4.8613 - 4.4172 1.00 1440 153 0.1502 0.2080 REMARK 3 5 4.4172 - 4.1008 1.00 1411 159 0.1609 0.1922 REMARK 3 6 4.1008 - 3.8591 1.00 1425 164 0.1792 0.2480 REMARK 3 7 3.8591 - 3.6659 1.00 1416 155 0.1760 0.2064 REMARK 3 8 3.6659 - 3.5064 1.00 1423 160 0.1752 0.2429 REMARK 3 9 3.5064 - 3.3715 1.00 1413 158 0.1920 0.1931 REMARK 3 10 3.3715 - 3.2552 1.00 1422 157 0.2010 0.2458 REMARK 3 11 3.2552 - 3.1534 1.00 1425 152 0.2016 0.2564 REMARK 3 12 3.1534 - 3.0633 1.00 1429 156 0.2287 0.2690 REMARK 3 13 3.0633 - 2.9827 1.00 1413 160 0.2343 0.2803 REMARK 3 14 2.9827 - 2.9099 1.00 1422 162 0.2126 0.2725 REMARK 3 15 2.9099 - 2.8438 1.00 1444 159 0.2147 0.2848 REMARK 3 16 2.8438 - 2.7832 1.00 1404 158 0.2279 0.3308 REMARK 3 17 2.7832 - 2.7276 1.00 1438 161 0.2462 0.3022 REMARK 3 18 2.7276 - 2.6761 1.00 1384 152 0.2561 0.3265 REMARK 3 19 2.6761 - 2.6283 0.99 1436 160 0.2738 0.2958 REMARK 3 20 2.6283 - 2.5838 0.95 1345 148 0.2573 0.3402 REMARK 3 21 2.5838 - 2.5421 0.83 1187 135 0.2708 0.3054 REMARK 3 22 2.5421 - 2.5030 0.68 967 105 0.2668 0.3579 REMARK 3 23 2.5030 - 2.4662 0.48 676 75 0.2815 0.3206 REMARK 3 24 2.4662 - 2.4314 0.33 459 55 0.2950 0.3519 REMARK 3 25 2.4314 - 2.3986 0.19 267 29 0.2728 0.4692 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.009 2627 REMARK 3 ANGLE : 1.104 3553 REMARK 3 CHIRALITY : 0.061 414 REMARK 3 PLANARITY : 0.006 454 REMARK 3 DIHEDRAL : 4.701 1618 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I_MINUS AND I_PLUS COLUMNS. REMARK 4 REMARK 4 6JTG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-19. REMARK 100 THE DEPOSITION ID IS D_1300011777. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21509 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM THIOCYANATE AND REMARK 280 20%(W/V) POLYETHYLENE GLYCOL 3350 (PH 7.0), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K 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 85.77350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.94500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.94500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 128.66025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.94500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.94500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.88675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.94500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.94500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 128.66025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.94500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.94500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.88675 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 85.77350 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: 6020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -85.77350 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 536 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 THR A 314 REMARK 465 GLU A 315 REMARK 465 TRP A 316 REMARK 465 LYS A 317 REMARK 465 ASN A 318 REMARK 465 GLY A 319 REMARK 465 SER A 320 REMARK 465 GLY A 321 REMARK 465 SER A 322 REMARK 465 GLY A 323 REMARK 465 SER A 324 REMARK 465 GLY A 325 REMARK 465 GLY A 326 REMARK 465 SER A 327 REMARK 465 ASP A 328 REMARK 465 LEU A 329 REMARK 465 LYS A 330 REMARK 465 LYS A 331 REMARK 465 GLU A 349 REMARK 465 LYS A 350 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 270 OG REMARK 470 GLU A 313 CG CD OE1 OE2 REMARK 470 VAL A 332 CG1 CG2 REMARK 470 ARG A 333 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 334 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH1 ARG A 104 O HOH A 501 1.86 REMARK 500 O ALA A 238 O VAL A 277 1.87 REMARK 500 OG1 THR A 278 O HOH A 502 1.91 REMARK 500 O GLN A 301 CD2 PHE A 305 2.04 REMARK 500 O PHE A 305 OG1 THR A 308 2.11 REMARK 500 CE2 PHE A 305 CD1 LEU A 339 2.13 REMARK 500 O HOH A 504 O HOH A 583 2.14 REMARK 500 O HOH A 580 O HOH A 625 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CB SER A 246 CD2 LEU A 312 5444 0.49 REMARK 500 OG SER A 246 CD2 LEU A 312 5444 1.02 REMARK 500 CB SER A 246 CG LEU A 312 5444 1.57 REMARK 500 OD1 ASN A 245 O ASN A 311 5444 1.91 REMARK 500 CA SER A 246 CD2 LEU A 312 5444 1.91 REMARK 500 CG ASN A 245 O ASN A 311 5444 1.97 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 6 CD1 TYR A 6 CE1 -0.101 REMARK 500 TYR A 6 CE2 TYR A 6 CD2 -0.099 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 LEU A 2 CB - CG - CD2 ANGL. DEV. = -13.1 DEGREES REMARK 500 TYR A 16 CB - CA - C ANGL. DEV. = -15.3 DEGREES REMARK 500 ASP A 17 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 LEU A 346 CB - CA - C ANGL. DEV. = -17.9 DEGREES REMARK 500 HIS A 347 N - CA - CB ANGL. DEV. = -23.7 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 LEU A 13 2.08 -67.48 REMARK 500 ASP A 15 -76.83 69.17 REMARK 500 ALA A 18 72.37 80.01 REMARK 500 ARG A 199 31.10 -144.04 REMARK 500 ASN A 213 -22.94 -140.80 REMARK 500 SER A 216 86.82 -157.81 REMARK 500 GLN A 300 -9.07 -58.54 REMARK 500 LEU A 312 -82.25 -109.65 REMARK 500 ARG A 333 -72.71 -74.92 REMARK 500 HIS A 347 70.90 -69.31 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 GLN A 301 ALA A 302 142.48 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 K A 404 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 36 OG REMARK 620 2 GLY A 55 O 83.6 REMARK 620 3 GLU A 58 O 82.0 86.1 REMARK 620 4 GDP A 401 O1B 107.7 140.8 131.9 REMARK 620 5 GDP A 401 O1A 123.5 72.2 142.8 70.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 40 OG1 REMARK 620 2 THR A 61 OG1 99.4 REMARK 620 3 GDP A 401 O3B 85.5 158.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF A 403 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GDP A 401 O1B REMARK 620 2 BEF A 403 F1 104.1 REMARK 620 3 BEF A 403 F2 106.0 117.1 REMARK 620 4 BEF A 403 F3 95.4 115.9 114.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BEF A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 404 DBREF 6JTG A 1 309 UNP O60313 OPA1_HUMAN 267 575 DBREF 6JTG A 328 350 UNP Q6PEK6 Q6PEK6_HUMAN 254 276 SEQADV 6JTG PHE A 310 UNP O60313 LINKER SEQADV 6JTG ASN A 311 UNP O60313 LINKER SEQADV 6JTG LEU A 312 UNP O60313 LINKER SEQADV 6JTG GLU A 313 UNP O60313 LINKER SEQADV 6JTG THR A 314 UNP O60313 LINKER SEQADV 6JTG GLU A 315 UNP O60313 LINKER SEQADV 6JTG TRP A 316 UNP O60313 LINKER SEQADV 6JTG LYS A 317 UNP O60313 LINKER SEQADV 6JTG ASN A 318 UNP O60313 LINKER SEQADV 6JTG GLY A 319 UNP O60313 LINKER SEQADV 6JTG SER A 320 UNP O60313 LINKER SEQADV 6JTG GLY A 321 UNP O60313 LINKER SEQADV 6JTG SER A 322 UNP O60313 LINKER SEQADV 6JTG GLY A 323 UNP O60313 LINKER SEQADV 6JTG SER A 324 UNP O60313 LINKER SEQADV 6JTG GLY A 325 UNP O60313 LINKER SEQADV 6JTG GLY A 326 UNP O60313 LINKER SEQADV 6JTG SER A 327 UNP O60313 LINKER SEQRES 1 A 350 SER LEU ILE ASP MET TYR SER GLU VAL LEU ASP VAL LEU SEQRES 2 A 350 SER ASP TYR ASP ALA SER TYR ASN THR GLN ASP HIS LEU SEQRES 3 A 350 PRO ARG VAL VAL VAL VAL GLY ASP GLN SER ALA GLY LYS SEQRES 4 A 350 THR SER VAL LEU GLU MET ILE ALA GLN ALA ARG ILE PHE SEQRES 5 A 350 PRO ARG GLY SER GLY GLU MET MET THR ARG SER PRO VAL SEQRES 6 A 350 LYS VAL THR LEU SER GLU GLY PRO HIS HIS VAL ALA LEU SEQRES 7 A 350 PHE LYS ASP SER SER ARG GLU PHE ASP LEU THR LYS GLU SEQRES 8 A 350 GLU ASP LEU ALA ALA LEU ARG HIS GLU ILE GLU LEU ARG SEQRES 9 A 350 MET ARG LYS ASN VAL LYS GLU GLY CYS THR VAL SER PRO SEQRES 10 A 350 GLU THR ILE SER LEU ASN VAL LYS GLY PRO GLY LEU GLN SEQRES 11 A 350 ARG MET VAL LEU VAL ASP LEU PRO GLY VAL ILE ASN THR SEQRES 12 A 350 VAL THR SER GLY MET ALA PRO ASP THR LYS GLU THR ILE SEQRES 13 A 350 PHE SER ILE SER LYS ALA TYR MET GLN ASN PRO ASN ALA SEQRES 14 A 350 ILE ILE LEU CYS ILE GLN ASP GLY SER VAL ASP ALA GLU SEQRES 15 A 350 ARG SER ILE VAL THR ASP LEU VAL SER GLN MET ASP PRO SEQRES 16 A 350 HIS GLY ARG ARG THR ILE PHE VAL LEU THR LYS VAL ASP SEQRES 17 A 350 LEU ALA GLU LYS ASN VAL ALA SER PRO SER ARG ILE GLN SEQRES 18 A 350 GLN ILE ILE GLU GLY LYS LEU PHE PRO MET LYS ALA LEU SEQRES 19 A 350 GLY TYR PHE ALA VAL VAL THR GLY LYS GLY ASN SER SER SEQRES 20 A 350 GLU SER ILE GLU ALA ILE ARG GLU TYR GLU GLU GLU PHE SEQRES 21 A 350 PHE GLN ASN SER LYS LEU LEU LYS THR SER MET LEU LYS SEQRES 22 A 350 ALA HIS GLN VAL THR THR ARG ASN LEU SER LEU ALA VAL SEQRES 23 A 350 SER ASP CYS PHE TRP LYS MET VAL ARG GLU SER VAL GLU SEQRES 24 A 350 GLN GLN ALA ASP SER PHE LYS ALA THR ARG PHE ASN LEU SEQRES 25 A 350 GLU THR GLU TRP LYS ASN GLY SER GLY SER GLY SER GLY SEQRES 26 A 350 GLY SER ASP LEU LYS LYS VAL ARG GLU ILE GLN GLU LYS SEQRES 27 A 350 LEU ASP ALA PHE ILE GLU ALA LEU HIS GLN GLU LYS HET GDP A 401 28 HET MG A 402 1 HET BEF A 403 4 HET K A 404 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM BEF BERYLLIUM TRIFLUORIDE ION HETNAM K POTASSIUM ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 BEF BE F3 1- FORMUL 5 K K 1+ FORMUL 6 HOH *142(H2 O) HELIX 1 AA1 SER A 1 LEU A 13 1 13 HELIX 2 AA2 GLY A 38 GLN A 48 1 11 HELIX 3 AA3 LYS A 90 VAL A 109 1 20 HELIX 4 AA4 ASP A 151 GLN A 165 1 15 HELIX 5 AA5 ASP A 180 SER A 184 5 5 HELIX 6 AA6 VAL A 186 ASP A 194 1 9 HELIX 7 AA7 LYS A 206 VAL A 214 1 9 HELIX 8 AA8 SER A 216 GLU A 225 1 10 HELIX 9 AA9 SER A 249 ASN A 263 1 15 HELIX 10 AB1 SER A 264 THR A 269 1 6 HELIX 11 AB2 THR A 278 VAL A 298 1 21 HELIX 12 AB3 VAL A 298 LEU A 312 1 15 HELIX 13 AB4 GLU A 334 HIS A 347 1 14 SHEET 1 AA1 9 PHE A 86 ASP A 87 0 SHEET 2 AA1 9 VAL A 76 PHE A 79 -1 N ALA A 77 O PHE A 86 SHEET 3 AA1 9 ILE A 120 GLY A 126 -1 O ASN A 123 N LEU A 78 SHEET 4 AA1 9 VAL A 65 GLU A 71 1 N THR A 68 O VAL A 124 SHEET 5 AA1 9 MET A 132 ASP A 136 -1 O LEU A 134 N VAL A 67 SHEET 6 AA1 9 VAL A 29 GLY A 33 1 N VAL A 29 O VAL A 133 SHEET 7 AA1 9 ILE A 170 ASP A 176 1 O ILE A 170 N VAL A 30 SHEET 8 AA1 9 THR A 200 THR A 205 1 O VAL A 203 N GLN A 175 SHEET 9 AA1 9 GLY A 235 ALA A 238 1 O PHE A 237 N LEU A 204 LINK OG SER A 36 K K A 404 1555 1555 2.73 LINK OG1 THR A 40 MG MG A 402 1555 1555 1.86 LINK O GLY A 55 K K A 404 1555 1555 2.68 LINK O GLU A 58 K K A 404 1555 1555 2.96 LINK OG1 THR A 61 MG MG A 402 1555 1555 2.18 LINK O3B GDP A 401 MG MG A 402 1555 1555 2.32 LINK O1B GDP A 401 BE BEF A 403 1555 1555 1.72 LINK O1B GDP A 401 K K A 404 1555 1555 2.72 LINK O1A GDP A 401 K K A 404 1555 1555 3.28 CISPEP 1 SER A 14 ASP A 15 0 -14.30 SITE 1 AC1 23 SER A 36 ALA A 37 GLY A 38 LYS A 39 SITE 2 AC1 23 THR A 40 SER A 41 ARG A 54 GLY A 55 SITE 3 AC1 23 SER A 56 LYS A 206 ASP A 208 LEU A 209 SITE 4 AC1 23 VAL A 240 THR A 241 GLY A 242 LYS A 243 SITE 5 AC1 23 GLY A 244 MG A 402 BEF A 403 K A 404 SITE 6 AC1 23 HOH A 506 HOH A 519 HOH A 565 SITE 1 AC2 5 THR A 40 THR A 61 ASP A 136 GDP A 401 SITE 2 AC2 5 BEF A 403 SITE 1 AC3 10 GLN A 35 SER A 36 LYS A 39 MET A 60 SITE 2 AC3 10 THR A 61 GLY A 139 GDP A 401 MG A 402 SITE 3 AC3 10 K A 404 HOH A 517 SITE 1 AC4 5 SER A 36 GLY A 55 GLU A 58 GDP A 401 SITE 2 AC4 5 BEF A 403 CRYST1 77.890 77.890 171.547 90.00 90.00 90.00 P 43 21 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 0.012839 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005829 0.00000