HEADER SIGNALING PROTEIN 08-NOV-21 7Q6J TITLE CRYSTAL STRUCTURE OF THE HUMAN GDAP1 CMT2 MUTANT-H123R COMPND MOL_ID: 1; COMPND 2 MOLECULE: GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GDAP1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GDAP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTH-27 KEYWDS CHARCOT-MARIE-TOOTH, CMT2, MUTATION, MITOCHONDRIA, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SUTINEN,P.KURSULA REVDAT 4 31-JAN-24 7Q6J 1 REMARK REVDAT 3 13-JUL-22 7Q6J 1 JRNL REVDAT 2 15-JUN-22 7Q6J 1 JRNL REVDAT 1 08-JUN-22 7Q6J 0 JRNL AUTH A.SUTINEN,G.T.T.NGUYEN,A.RAASAKKA,G.MURUGANANDAM,R.LORIS, JRNL AUTH 2 E.YLIKALLIO,H.TYYNISMAA,L.BARTESAGHI,S.RUSKAMO,P.KURSULA JRNL TITL STRUCTURAL INSIGHTS INTO CHARCOT-MARIE-TOOTH DISEASE-LINKED JRNL TITL 2 MUTATIONS IN HUMAN GDAP1. JRNL REF FEBS OPEN BIO V. 12 1306 2022 JRNL REFN ESSN 2211-5463 JRNL PMID 35509130 JRNL DOI 10.1002/2211-5463.13422 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18-3861 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 50401 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 45.3800 - 5.3000 1.00 3672 147 0.1949 0.2171 REMARK 3 2 5.3000 - 4.2100 1.00 3541 146 0.1715 0.1922 REMARK 3 3 4.2100 - 3.6800 1.00 3501 144 0.1929 0.1822 REMARK 3 4 3.6800 - 3.3400 1.00 3456 141 0.2168 0.2448 REMARK 3 5 3.3400 - 3.1000 1.00 3460 144 0.2257 0.2421 REMARK 3 6 3.1000 - 2.9200 1.00 3453 142 0.2385 0.2873 REMARK 3 7 2.9200 - 2.7700 1.00 3447 142 0.2623 0.2831 REMARK 3 8 2.7700 - 2.6500 1.00 3428 142 0.2482 0.2949 REMARK 3 9 2.6500 - 2.5500 1.00 3431 140 0.2416 0.2730 REMARK 3 10 2.5500 - 2.4600 1.00 3439 144 0.2410 0.2915 REMARK 3 11 2.4600 - 2.3800 1.00 3404 142 0.2666 0.3032 REMARK 3 12 2.3800 - 2.3200 1.00 3414 139 0.2823 0.3262 REMARK 3 13 2.3200 - 2.2600 0.99 3406 137 0.3294 0.3361 REMARK 3 14 2.2600 - 2.2000 0.99 3359 140 0.3985 0.4132 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 59.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.19 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 23 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.4888 -37.3867 23.7586 REMARK 3 T TENSOR REMARK 3 T11: 0.4682 T22: 0.4810 REMARK 3 T33: 0.4268 T12: -0.0243 REMARK 3 T13: -0.0490 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 1.9168 L22: 1.1346 REMARK 3 L33: 0.7626 L12: -1.3076 REMARK 3 L13: 0.9749 L23: -0.6507 REMARK 3 S TENSOR REMARK 3 S11: 0.1200 S12: -0.2397 S13: -0.1442 REMARK 3 S21: 0.1842 S22: -0.0812 S23: -0.1072 REMARK 3 S31: 0.0694 S32: -0.0812 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.7703 -23.8319 10.0108 REMARK 3 T TENSOR REMARK 3 T11: 0.4023 T22: 0.4209 REMARK 3 T33: 0.3478 T12: 0.0330 REMARK 3 T13: 0.0144 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 1.6852 L22: 1.2080 REMARK 3 L33: 1.1902 L12: 0.2600 REMARK 3 L13: -0.0319 L23: 0.3911 REMARK 3 S TENSOR REMARK 3 S11: 0.1474 S12: 0.0980 S13: 0.0321 REMARK 3 S21: -0.0171 S22: 0.0421 S23: 0.0121 REMARK 3 S31: -0.1286 S32: -0.0492 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 23 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.3481 -43.3592 29.7313 REMARK 3 T TENSOR REMARK 3 T11: 0.4286 T22: 0.3893 REMARK 3 T33: 0.5115 T12: -0.0258 REMARK 3 T13: -0.0814 T23: 0.0918 REMARK 3 L TENSOR REMARK 3 L11: 1.8057 L22: 1.2750 REMARK 3 L33: 0.6532 L12: -1.3177 REMARK 3 L13: 0.3112 L23: -0.6477 REMARK 3 S TENSOR REMARK 3 S11: -0.0331 S12: -0.0998 S13: 0.0502 REMARK 3 S21: -0.2561 S22: -0.0298 S23: -0.4723 REMARK 3 S31: -0.0083 S32: -0.0623 S33: -0.0005 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 116 THROUGH 153 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5818 -52.9351 17.8362 REMARK 3 T TENSOR REMARK 3 T11: 1.0316 T22: 0.6881 REMARK 3 T33: 0.7985 T12: 0.1200 REMARK 3 T13: 0.3282 T23: 0.2472 REMARK 3 L TENSOR REMARK 3 L11: 0.5991 L22: 0.2588 REMARK 3 L33: 0.3582 L12: -0.1489 REMARK 3 L13: 0.1022 L23: -0.2970 REMARK 3 S TENSOR REMARK 3 S11: 0.2964 S12: 0.2764 S13: 0.6076 REMARK 3 S21: -1.3446 S22: -0.4944 S23: -0.5286 REMARK 3 S31: 0.2400 S32: 0.2533 S33: -0.1134 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 154 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.6360 -54.4170 18.5558 REMARK 3 T TENSOR REMARK 3 T11: 0.8358 T22: 0.5813 REMARK 3 T33: 0.9629 T12: 0.1127 REMARK 3 T13: 0.4482 T23: 0.2702 REMARK 3 L TENSOR REMARK 3 L11: 0.8660 L22: 1.6079 REMARK 3 L33: 0.7947 L12: -1.1392 REMARK 3 L13: 0.0308 L23: -0.4472 REMARK 3 S TENSOR REMARK 3 S11: 0.0899 S12: 0.5599 S13: 0.6871 REMARK 3 S21: -0.6932 S22: -0.2220 S23: -1.0396 REMARK 3 S31: 0.3505 S32: 0.5014 S33: -0.0091 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 246 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.2695 -55.9790 27.9234 REMARK 3 T TENSOR REMARK 3 T11: 0.5427 T22: 0.5309 REMARK 3 T33: 0.9225 T12: -0.0097 REMARK 3 T13: 0.1906 T23: 0.1669 REMARK 3 L TENSOR REMARK 3 L11: 0.5652 L22: 0.9638 REMARK 3 L33: 0.2760 L12: -0.6938 REMARK 3 L13: 0.4319 L23: -0.3937 REMARK 3 S TENSOR REMARK 3 S11: -0.0650 S12: -0.1755 S13: 0.3012 REMARK 3 S21: -0.2076 S22: -0.0818 S23: -1.3125 REMARK 3 S31: 0.1049 S32: 0.2500 S33: -0.0244 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 23 THROUGH 30 OR REMARK 3 RESID 32 THROUGH 35 OR RESID 37 THROUGH REMARK 3 40 OR RESID 42 THROUGH 63 OR RESID 65 REMARK 3 THROUGH 137 OR RESID 139 THROUGH 160 OR REMARK 3 RESID 191 OR RESID 194 OR RESID 197 REMARK 3 THROUGH 224 OR RESID 226 THROUGH 302)) REMARK 3 SELECTION : (CHAIN B AND (RESID 23 THROUGH 30 OR REMARK 3 RESID 32 THROUGH 35 OR RESID 37 THROUGH REMARK 3 40 OR RESID 42 THROUGH 63 OR RESID 65 REMARK 3 THROUGH 137 OR RESID 139 THROUGH 162 OR REMARK 3 RESID 197 THROUGH 224 OR RESID 226 REMARK 3 THROUGH 302)) REMARK 3 ATOM PAIRS NUMBER : 2313 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7Q6J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292119099. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SILICON REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS FEB 5, 2021 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50431 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 45.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.515 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.66 REMARK 200 R MERGE FOR SHELL (I) : 1.60200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.430 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 7ALM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, DL-MALIC ACID, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 36.35500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.09000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.94000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.09000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.35500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.94000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 ARG A 161 REMARK 465 SER A 162 REMARK 465 GLN A 163 REMARK 465 ILE A 164 REMARK 465 GLY A 165 REMARK 465 ASN A 166 REMARK 465 THR A 167 REMARK 465 GLU A 168 REMARK 465 SER A 169 REMARK 465 GLU A 170 REMARK 465 LEU A 171 REMARK 465 LYS A 172 REMARK 465 LYS A 173 REMARK 465 LEU A 174 REMARK 465 ALA A 175 REMARK 465 GLU A 176 REMARK 465 GLU A 177 REMARK 465 ASN A 178 REMARK 465 PRO A 179 REMARK 465 ASP A 180 REMARK 465 LEU A 181 REMARK 465 GLN A 182 REMARK 465 GLU A 183 REMARK 465 GLY B 165 REMARK 465 ASN B 166 REMARK 465 THR B 167 REMARK 465 GLU B 168 REMARK 465 SER B 169 REMARK 465 GLU B 170 REMARK 465 LEU B 171 REMARK 465 LYS B 172 REMARK 465 LYS B 173 REMARK 465 LEU B 174 REMARK 465 ALA B 175 REMARK 465 GLU B 176 REMARK 465 GLU B 177 REMARK 465 ASN B 178 REMARK 465 PRO B 179 REMARK 465 ASP B 180 REMARK 465 LEU B 181 REMARK 465 GLN B 182 REMARK 465 GLU B 183 REMARK 465 ALA B 184 REMARK 465 TYR B 185 REMARK 465 ILE B 186 REMARK 465 ALA B 187 REMARK 465 LYS B 188 REMARK 465 GLN B 189 REMARK 465 LYS B 190 REMARK 465 ARG B 191 REMARK 465 LEU B 192 REMARK 465 LYS B 193 REMARK 465 SER B 194 REMARK 465 LYS B 195 REMARK 465 LEU B 196 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 HZ1 LYS B 47 OE1 GLU B 98 1.56 REMARK 500 OE2 GLU A 222 NH2 ARG A 226 2.17 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 226 CG - CD - NE ANGL. DEV. = -13.5 DEGREES REMARK 500 ASN B 227 O - C - N ANGL. DEV. = -9.9 DEGREES REMARK 500 GLU B 232 OE1 - CD - OE2 ANGL. DEV. = -10.8 DEGREES REMARK 500 GLU B 232 CG - CD - OE1 ANGL. DEV. = 16.1 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 VAL A 24 89.23 45.52 REMARK 500 HIS A 63 33.42 -86.07 REMARK 500 GLU A 76 86.95 -150.66 REMARK 500 GLU A 89 144.18 81.56 REMARK 500 ASP A 103 150.15 -49.17 REMARK 500 TYR A 185 -120.08 57.47 REMARK 500 ARG A 273 65.93 36.62 REMARK 500 ASN B 72 18.64 51.28 REMARK 500 THR B 74 -53.29 93.31 REMARK 500 GLU B 89 139.54 80.78 REMARK 500 ARG B 161 -52.32 178.68 REMARK 500 TRP B 238 -158.77 -98.07 REMARK 500 ARG B 273 63.45 35.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ALM RELATED DB: PDB REMARK 900 RELATED ID: 7AIA RELATED DB: PDB DBREF 7Q6J A 23 302 UNP Q8TB36 GDAP1_HUMAN 23 302 DBREF 7Q6J B 23 302 UNP Q8TB36 GDAP1_HUMAN 23 302 SEQADV 7Q6J ARG A 123 UNP Q8TB36 HIS 123 ENGINEERED MUTATION SEQADV 7Q6J ARG B 123 UNP Q8TB36 HIS 123 ENGINEERED MUTATION SEQRES 1 A 280 GLU VAL LYS LEU ILE LEU TYR HIS TRP THR HIS SER PHE SEQRES 2 A 280 SER SER GLN LYS VAL ARG LEU VAL ILE ALA GLU LYS ALA SEQRES 3 A 280 LEU LYS CYS GLU GLU HIS ASP VAL SER LEU PRO LEU SER SEQRES 4 A 280 GLU HIS ASN GLU PRO TRP PHE MET ARG LEU ASN SER THR SEQRES 5 A 280 GLY GLU VAL PRO VAL LEU ILE HIS GLY GLU ASN ILE ILE SEQRES 6 A 280 CYS GLU ALA THR GLN ILE ILE ASP TYR LEU GLU GLN THR SEQRES 7 A 280 PHE LEU ASP GLU ARG THR PRO ARG LEU MET PRO ASP LYS SEQRES 8 A 280 GLU SER MET TYR TYR PRO ARG VAL GLN ARG TYR ARG GLU SEQRES 9 A 280 LEU LEU ASP SER LEU PRO MET ASP ALA TYR THR HIS GLY SEQRES 10 A 280 CYS ILE LEU HIS PRO GLU LEU THR VAL ASP SER MET ILE SEQRES 11 A 280 PRO ALA TYR ALA THR THR ARG ILE ARG SER GLN ILE GLY SEQRES 12 A 280 ASN THR GLU SER GLU LEU LYS LYS LEU ALA GLU GLU ASN SEQRES 13 A 280 PRO ASP LEU GLN GLU ALA TYR ILE ALA LYS GLN LYS ARG SEQRES 14 A 280 LEU LYS SER LYS LEU LEU ASP HIS ASP ASN VAL LYS TYR SEQRES 15 A 280 LEU LYS LYS ILE LEU ASP GLU LEU GLU LYS VAL LEU ASP SEQRES 16 A 280 GLN VAL GLU THR GLU LEU GLN ARG ARG ASN GLU GLU THR SEQRES 17 A 280 PRO GLU GLU GLY GLN GLN PRO TRP LEU CYS GLY GLU SER SEQRES 18 A 280 PHE THR LEU ALA ASP VAL SER LEU ALA VAL THR LEU HIS SEQRES 19 A 280 ARG LEU LYS PHE LEU GLY PHE ALA ARG ARG ASN TRP GLY SEQRES 20 A 280 ASN GLY LYS ARG PRO ASN LEU GLU THR TYR TYR GLU ARG SEQRES 21 A 280 VAL LEU LYS ARG LYS THR PHE ASN LYS VAL LEU GLY HIS SEQRES 22 A 280 VAL ASN ASN ILE LEU ILE SER SEQRES 1 B 280 GLU VAL LYS LEU ILE LEU TYR HIS TRP THR HIS SER PHE SEQRES 2 B 280 SER SER GLN LYS VAL ARG LEU VAL ILE ALA GLU LYS ALA SEQRES 3 B 280 LEU LYS CYS GLU GLU HIS ASP VAL SER LEU PRO LEU SER SEQRES 4 B 280 GLU HIS ASN GLU PRO TRP PHE MET ARG LEU ASN SER THR SEQRES 5 B 280 GLY GLU VAL PRO VAL LEU ILE HIS GLY GLU ASN ILE ILE SEQRES 6 B 280 CYS GLU ALA THR GLN ILE ILE ASP TYR LEU GLU GLN THR SEQRES 7 B 280 PHE LEU ASP GLU ARG THR PRO ARG LEU MET PRO ASP LYS SEQRES 8 B 280 GLU SER MET TYR TYR PRO ARG VAL GLN ARG TYR ARG GLU SEQRES 9 B 280 LEU LEU ASP SER LEU PRO MET ASP ALA TYR THR HIS GLY SEQRES 10 B 280 CYS ILE LEU HIS PRO GLU LEU THR VAL ASP SER MET ILE SEQRES 11 B 280 PRO ALA TYR ALA THR THR ARG ILE ARG SER GLN ILE GLY SEQRES 12 B 280 ASN THR GLU SER GLU LEU LYS LYS LEU ALA GLU GLU ASN SEQRES 13 B 280 PRO ASP LEU GLN GLU ALA TYR ILE ALA LYS GLN LYS ARG SEQRES 14 B 280 LEU LYS SER LYS LEU LEU ASP HIS ASP ASN VAL LYS TYR SEQRES 15 B 280 LEU LYS LYS ILE LEU ASP GLU LEU GLU LYS VAL LEU ASP SEQRES 16 B 280 GLN VAL GLU THR GLU LEU GLN ARG ARG ASN GLU GLU THR SEQRES 17 B 280 PRO GLU GLU GLY GLN GLN PRO TRP LEU CYS GLY GLU SER SEQRES 18 B 280 PHE THR LEU ALA ASP VAL SER LEU ALA VAL THR LEU HIS SEQRES 19 B 280 ARG LEU LYS PHE LEU GLY PHE ALA ARG ARG ASN TRP GLY SEQRES 20 B 280 ASN GLY LYS ARG PRO ASN LEU GLU THR TYR TYR GLU ARG SEQRES 21 B 280 VAL LEU LYS ARG LYS THR PHE ASN LYS VAL LEU GLY HIS SEQRES 22 B 280 VAL ASN ASN ILE LEU ILE SER HET PEG A 401 17 HET PEG A 402 17 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 PEG 2(C4 H10 O3) FORMUL 5 HOH *93(H2 O) HELIX 1 AA1 SER A 34 LYS A 47 1 14 HELIX 2 AA2 PRO A 66 ARG A 70 5 5 HELIX 3 AA3 GLU A 89 PHE A 101 1 13 HELIX 4 AA4 TYR A 117 SER A 130 1 14 HELIX 5 AA5 PRO A 132 HIS A 143 1 12 HELIX 6 AA6 PRO A 144 THR A 147 5 4 HELIX 7 AA7 ALA A 154 ILE A 160 1 7 HELIX 8 AA8 TYR A 185 GLU A 229 1 45 HELIX 9 AA9 THR A 245 GLY A 262 1 18 HELIX 10 AB1 ARG A 273 ARG A 286 1 14 HELIX 11 AB2 ARG A 286 GLY A 294 1 9 HELIX 12 AB3 SER B 34 LYS B 47 1 14 HELIX 13 AB4 PRO B 66 ARG B 70 5 5 HELIX 14 AB5 GLU B 89 PHE B 101 1 13 HELIX 15 AB6 TYR B 117 SER B 130 1 14 HELIX 16 AB7 PRO B 132 HIS B 143 1 12 HELIX 17 AB8 PRO B 144 THR B 147 5 4 HELIX 18 AB9 ALA B 154 GLN B 163 1 10 HELIX 19 AC1 ASN B 201 THR B 230 1 30 HELIX 20 AC2 THR B 245 GLY B 262 1 18 HELIX 21 AC3 ARG B 273 ARG B 286 1 14 HELIX 22 AC4 ARG B 286 GLY B 294 1 9 SHEET 1 AA1 4 GLU A 52 ASP A 55 0 SHEET 2 AA1 4 LEU A 26 HIS A 30 1 N LEU A 28 O HIS A 54 SHEET 3 AA1 4 VAL A 79 HIS A 82 -1 O ILE A 81 N ILE A 27 SHEET 4 AA1 4 ASN A 85 CYS A 88 -1 O ILE A 87 N LEU A 80 SHEET 1 AA2 4 GLU B 52 ASP B 55 0 SHEET 2 AA2 4 LEU B 26 HIS B 30 1 N LEU B 28 O HIS B 54 SHEET 3 AA2 4 VAL B 79 HIS B 82 -1 O ILE B 81 N ILE B 27 SHEET 4 AA2 4 ASN B 85 CYS B 88 -1 O ILE B 87 N LEU B 80 SSBOND 1 CYS A 88 CYS B 88 1555 1555 2.13 CRYST1 72.710 115.880 116.180 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008630 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008607 0.00000