HEADER MEMBRANE PROTEIN 12-JUN-22 8A4K TITLE HUMAN GDAP1, R282H MUTANT 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 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GST FAMILY, MITOCHONDRIA, DISEASE MUTATION, DIMER, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SUTINEN,P.KURSULA REVDAT 2 07-FEB-24 8A4K 1 REMARK REVDAT 1 26-APR-23 8A4K 0 JRNL AUTH A.SUTINEN,D.PAFFENHOLZ,G.T.T.NGUYEN,S.RUSKAMO,A.E.TORDA, JRNL AUTH 2 P.KURSULA JRNL TITL CONSERVED INTRAMOLECULAR NETWORKS IN GDAP1 ARE CLOSELY JRNL TITL 2 CONNECTED TO CMT-LINKED MUTATIONS AND PROTEIN STABILITY. JRNL REF PLOS ONE V. 18 84532 2023 JRNL REFN ESSN 1932-6203 JRNL PMID 37058526 JRNL DOI 10.1371/JOURNAL.PONE.0284532 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 69656 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3770 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 44.8400 - 5.8500 0.98 4758 143 0.1896 0.1974 REMARK 3 2 5.8500 - 4.6400 1.00 4825 146 0.1812 0.2300 REMARK 3 3 4.6400 - 4.0600 1.00 4857 146 0.1673 0.1758 REMARK 3 4 4.0600 - 3.6800 1.00 4852 139 0.1946 0.2130 REMARK 3 5 3.6800 - 3.4200 1.00 4882 130 0.2016 0.2612 REMARK 3 6 3.4200 - 3.2200 1.00 4838 137 0.2355 0.2959 REMARK 3 7 3.2200 - 3.0600 0.98 4748 149 0.2328 0.2795 REMARK 3 8 3.0600 - 2.9300 0.97 4741 150 0.2454 0.2933 REMARK 3 9 2.9200 - 2.8100 1.00 4804 142 0.2422 0.2310 REMARK 3 10 2.8100 - 2.7200 1.00 4901 145 0.2331 0.2834 REMARK 3 11 2.7200 - 2.6300 1.00 4853 144 0.2246 0.2529 REMARK 3 12 2.6300 - 2.5600 1.00 4870 148 0.2392 0.2406 REMARK 3 13 2.5600 - 2.4900 1.00 4848 141 0.2445 0.2089 REMARK 3 14 2.4900 - 2.4300 1.00 4835 149 0.2443 0.2678 REMARK 3 15 2.4300 - 2.3700 1.00 4875 139 0.2863 0.3182 REMARK 3 16 2.3700 - 2.3200 1.00 4836 148 0.3370 0.3721 REMARK 3 17 2.3200 - 2.2800 1.00 4825 149 0.3459 0.3258 REMARK 3 18 2.2800 - 2.2300 1.00 4892 159 0.3519 0.3801 REMARK 3 19 2.2300 - 2.1900 1.00 4840 146 0.3808 0.4222 REMARK 3 20 2.1900 - 2.1600 0.98 4732 141 0.4025 0.4409 REMARK 3 21 2.1600 - 2.1200 0.96 4706 133 0.4379 0.4836 REMARK 3 22 2.1200 - 2.0900 0.98 4762 142 0.4739 0.4539 REMARK 3 23 2.0900 - 2.0600 0.98 4770 147 0.5097 0.5825 REMARK 3 24 2.0600 - 2.0300 0.97 4686 140 0.5437 0.5241 REMARK 3 25 2.0300 - 2.0000 0.93 4499 133 0.5855 0.5521 REMARK 3 26 2.0000 - 1.9700 0.80 3890 112 0.6481 0.5546 REMARK 3 27 1.9700 - 1.9500 0.51 2430 72 0.7280 0.7500 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.387 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.90 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 : 0.014 4169 REMARK 3 ANGLE : 1.371 5645 REMARK 3 CHIRALITY : 0.069 627 REMARK 3 PLANARITY : 0.016 720 REMARK 3 DIHEDRAL : 16.051 1583 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 23 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9613 0.1890 -13.8552 REMARK 3 T TENSOR REMARK 3 T11: 0.7588 T22: 0.7751 REMARK 3 T33: 0.7063 T12: 0.1774 REMARK 3 T13: 0.0657 T23: 0.1138 REMARK 3 L TENSOR REMARK 3 L11: 2.5951 L22: 0.8772 REMARK 3 L33: 1.4894 L12: 0.1007 REMARK 3 L13: 1.1342 L23: -0.1493 REMARK 3 S TENSOR REMARK 3 S11: 0.0433 S12: -0.1972 S13: 0.0278 REMARK 3 S21: 0.1284 S22: 0.0975 S23: 0.0212 REMARK 3 S31: 0.0046 S32: -0.2558 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 118 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.5633 -8.4296 -26.3565 REMARK 3 T TENSOR REMARK 3 T11: 0.8381 T22: 0.8925 REMARK 3 T33: 0.7611 T12: -0.1279 REMARK 3 T13: 0.0309 T23: 0.1772 REMARK 3 L TENSOR REMARK 3 L11: 1.9011 L22: 0.8770 REMARK 3 L33: 3.2672 L12: -0.6391 REMARK 3 L13: 1.1683 L23: -0.2589 REMARK 3 S TENSOR REMARK 3 S11: 0.1398 S12: -0.2700 S13: -0.1655 REMARK 3 S21: -0.1594 S22: 0.0213 S23: 0.2962 REMARK 3 S31: 0.5784 S32: -0.9364 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 23 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.0047 -5.0545 -8.9377 REMARK 3 T TENSOR REMARK 3 T11: 0.6465 T22: 0.6285 REMARK 3 T33: 0.6444 T12: 0.0681 REMARK 3 T13: 0.0739 T23: 0.0431 REMARK 3 L TENSOR REMARK 3 L11: 2.8745 L22: 1.5178 REMARK 3 L33: 1.5845 L12: -1.3497 REMARK 3 L13: 1.9224 L23: -1.0622 REMARK 3 S TENSOR REMARK 3 S11: 0.2035 S12: 0.1708 S13: 0.2569 REMARK 3 S21: -0.2065 S22: -0.1886 S23: -0.0086 REMARK 3 S31: -0.3077 S32: -0.1505 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 228 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.9152 -21.9973 7.0973 REMARK 3 T TENSOR REMARK 3 T11: 0.6269 T22: 0.6698 REMARK 3 T33: 0.6726 T12: -0.0525 REMARK 3 T13: 0.0104 T23: -0.0455 REMARK 3 L TENSOR REMARK 3 L11: 2.3438 L22: 0.8386 REMARK 3 L33: 0.8069 L12: 0.3247 REMARK 3 L13: -0.1801 L23: -0.0774 REMARK 3 S TENSOR REMARK 3 S11: 0.1464 S12: 0.1313 S13: -0.1799 REMARK 3 S21: 0.1523 S22: -0.2420 S23: 0.1478 REMARK 3 S31: -0.0594 S32: -0.2720 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 229 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.8552 -14.2361 1.7552 REMARK 3 T TENSOR REMARK 3 T11: 0.5987 T22: 0.5859 REMARK 3 T33: 0.6549 T12: -0.0215 REMARK 3 T13: -0.0193 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 2.5890 L22: 1.7502 REMARK 3 L33: 1.3040 L12: -0.1129 REMARK 3 L13: 0.0579 L23: -0.7441 REMARK 3 S TENSOR REMARK 3 S11: 0.1704 S12: -0.0157 S13: -0.1044 REMARK 3 S21: 0.1613 S22: -0.2694 S23: -0.2881 REMARK 3 S31: -0.0108 S32: 0.2986 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 23 through 72 or REMARK 3 resid 76 through 186 or resid 189 or REMARK 3 resid 199 through 229 or resid 235 REMARK 3 through 281 or resid 283 through 302)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 23 through 160 or REMARK 3 resid 163 through 281 or resid 283 REMARK 3 through 302)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8A4K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1292123638. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-21 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 : 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) : 1.03319 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70450 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.73800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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: 7ALM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SUCCINIC ACID; 20% (W/V) PEG REMARK 280 3350, VAPOR 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 36.63950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.59700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.68500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.59700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.63950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.68500 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 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 ILE A 160 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 ALA A 184 REMARK 465 TYR A 185 REMARK 465 SER B 73 REMARK 465 THR B 74 REMARK 465 GLY B 75 REMARK 465 ILE B 164 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 465 LEU B 197 REMARK 465 ASP B 198 REMARK 465 THR B 230 REMARK 465 PRO B 231 REMARK 465 GLU B 232 REMARK 465 GLU B 233 REMARK 465 GLY B 234 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 OE2 GLU A 222 HH22 ARG A 226 1.50 REMARK 500 OE2 GLU B 222 NH2 ARG B 226 1.89 REMARK 500 OE2 GLU A 222 NH2 ARG A 226 2.04 REMARK 500 O HOH A 450 O HOH A 454 2.14 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 GLU A 65 CB GLU A 65 CG -0.204 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. = -16.9 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 THR A 74 141.21 73.90 REMARK 500 GLU A 76 -86.69 69.45 REMARK 500 GLU A 89 149.42 81.53 REMARK 500 ASP A 103 142.19 -37.93 REMARK 500 TRP A 238 -161.20 -102.20 REMARK 500 ARG A 273 62.32 39.75 REMARK 500 GLU B 89 149.40 80.14 REMARK 500 PRO B 111 -80.04 -67.56 REMARK 500 TRP B 238 -163.01 -107.58 REMARK 500 ARG B 273 61.62 36.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 226 0.14 SIDE CHAIN REMARK 500 ARG A 257 0.09 SIDE CHAIN REMARK 500 ARG B 257 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7B2G RELATED DB: PDB REMARK 900 MUTANT R120Q REMARK 900 RELATED ID: 8A4J RELATED DB: PDB REMARK 900 MUTANT A247V DBREF 8A4K A 23 302 UNP Q8TB36 GDAP1_HUMAN 23 302 DBREF 8A4K B 23 302 UNP Q8TB36 GDAP1_HUMAN 23 302 SEQADV 8A4K HIS A 282 UNP Q8TB36 ARG 282 VARIANT SEQADV 8A4K HIS B 282 UNP Q8TB36 ARG 282 VARIANT 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 HIS 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 HIS 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 HIS 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 HIS 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 FORMUL 3 HOH *76(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 PRO A 153 ARG A 159 1 7 HELIX 8 AA8 ALA A 187 GLU A 229 1 43 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 LYS B 203 GLU B 229 1 27 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 2.09 CRYST1 73.279 113.370 115.194 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 0.013646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008681 0.00000 MTRIX1 1 -0.869534 0.492755 -0.033220 33.64331 1 MTRIX2 1 0.493813 0.868514 -0.042812 -9.48475 1 MTRIX3 1 0.007756 -0.053630 -0.998531 -23.60035 1