HEADER MEMBRANE PROTEIN 13-FEB-22 7YWD TITLE HUMAN GDAP1 CORE DOMAIN, TRIGONAL CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 1; COMPND 3 CHAIN: A, B, C, D; 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 HOMOLOGY, MITOCHONDRIAL OUTER MEMBRANE, CHARCOT-MARIE-TOOTH KEYWDS 2 DISEASE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.RAASAKKA,P.KURSULA REVDAT 4 31-JAN-24 7YWD 1 REMARK REVDAT 3 13-JUL-22 7YWD 1 JRNL REVDAT 2 15-JUN-22 7YWD 1 JRNL REVDAT 1 08-JUN-22 7YWD 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. 3.20 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 27686 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1360 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 59.0400 - 6.8900 1.00 2792 144 0.1858 0.2102 REMARK 3 2 6.8900 - 5.4700 1.00 2680 132 0.2829 0.3076 REMARK 3 3 5.4700 - 4.7800 1.00 2655 138 0.2493 0.2848 REMARK 3 4 4.7800 - 4.3400 1.00 2614 138 0.2443 0.2613 REMARK 3 5 4.3400 - 4.0300 1.00 2605 140 0.2737 0.2917 REMARK 3 6 4.0300 - 3.7900 1.00 2607 136 0.3076 0.3282 REMARK 3 7 3.7900 - 3.6000 1.00 2606 137 0.3456 0.3937 REMARK 3 8 3.6000 - 3.4500 1.00 2598 131 0.4078 0.3859 REMARK 3 9 3.4500 - 3.3100 1.00 2588 137 0.3858 0.4261 REMARK 3 10 3.3100 - 3.2000 1.00 2581 127 0.4108 0.4555 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) : 0.645 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.711 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 144.8 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 188.4 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 : 0.003 8403 REMARK 3 ANGLE : 0.607 11361 REMARK 3 CHIRALITY : 0.037 1258 REMARK 3 PLANARITY : 0.004 1449 REMARK 3 DIHEDRAL : 15.982 3221 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 23 THROUGH 294) REMARK 3 ORIGIN FOR THE GROUP (A): 42.4976 -46.8668 -43.9634 REMARK 3 T TENSOR REMARK 3 T11: 1.4812 T22: 0.9346 REMARK 3 T33: 1.1477 T12: 0.2866 REMARK 3 T13: 0.1114 T23: 0.1121 REMARK 3 L TENSOR REMARK 3 L11: 6.1899 L22: 2.6818 REMARK 3 L33: 2.9882 L12: 0.9598 REMARK 3 L13: 0.4568 L23: 0.8419 REMARK 3 S TENSOR REMARK 3 S11: 0.5584 S12: 0.3693 S13: 0.4873 REMARK 3 S21: 0.0414 S22: -0.1541 S23: -0.3923 REMARK 3 S31: -0.0095 S32: 0.1648 S33: -0.4361 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 23 THROUGH 294) REMARK 3 ORIGIN FOR THE GROUP (A): 24.4467 -26.6913 -20.2679 REMARK 3 T TENSOR REMARK 3 T11: 1.1957 T22: 0.8406 REMARK 3 T33: 1.2623 T12: -0.1348 REMARK 3 T13: 0.1634 T23: -0.2868 REMARK 3 L TENSOR REMARK 3 L11: 5.9391 L22: 4.8855 REMARK 3 L33: 6.0598 L12: 0.5479 REMARK 3 L13: -2.0238 L23: 1.2664 REMARK 3 S TENSOR REMARK 3 S11: 0.6516 S12: -0.6346 S13: 0.7621 REMARK 3 S21: -0.1897 S22: 0.1799 S23: -0.5932 REMARK 3 S31: -0.5846 S32: 0.9379 S33: -0.7870 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 23 THROUGH 294) REMARK 3 ORIGIN FOR THE GROUP (A): 13.8993 -57.0110 1.8529 REMARK 3 T TENSOR REMARK 3 T11: 1.2111 T22: 1.5356 REMARK 3 T33: 1.6227 T12: -0.2705 REMARK 3 T13: -0.2741 T23: 0.2780 REMARK 3 L TENSOR REMARK 3 L11: 2.5220 L22: 7.6906 REMARK 3 L33: 3.0864 L12: 0.5584 REMARK 3 L13: 0.5364 L23: -0.0480 REMARK 3 S TENSOR REMARK 3 S11: 0.5823 S12: -0.8104 S13: -0.9482 REMARK 3 S21: 1.0093 S22: -0.6011 S23: -0.7726 REMARK 3 S31: 0.4689 S32: 0.4269 S33: 0.0487 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 23 THROUGH 294) REMARK 3 ORIGIN FOR THE GROUP (A): 21.6425 1.5240 5.1426 REMARK 3 T TENSOR REMARK 3 T11: 1.8381 T22: 2.0985 REMARK 3 T33: 2.2417 T12: -0.5552 REMARK 3 T13: 0.2602 T23: -0.9726 REMARK 3 L TENSOR REMARK 3 L11: 3.7498 L22: 3.3434 REMARK 3 L33: 2.9877 L12: -1.8026 REMARK 3 L13: -0.6023 L23: 1.8900 REMARK 3 S TENSOR REMARK 3 S11: 0.0623 S12: -1.0938 S13: 1.0248 REMARK 3 S21: -0.2789 S22: 0.8540 S23: -1.2626 REMARK 3 S31: -0.7742 S32: 1.2161 S33: -0.7749 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 68 or REMARK 3 resid 77 through 164 or resid 194 through REMARK 3 294)) 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 164 or REMARK 3 resid 194 through 294)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 3 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "C" and (resid 23 through 68 or REMARK 3 resid 77 through 164 or resid 194 through REMARK 3 294)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 4 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "D" and (resid 23 through 68 or REMARK 3 resid 77 through 164 or resid 194 through REMARK 3 294)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7YWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292121038. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-16 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, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) 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 : NULL 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 : 27737 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 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 (%): 61.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM NH4 FORMATE, 25% PEG3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.04000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 118.08000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 118.08000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 59.04000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -118.08000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 70 REMARK 465 LEU A 71 REMARK 465 ASN A 72 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 ILE A 186 REMARK 465 ALA A 187 REMARK 465 LYS A 188 REMARK 465 GLN A 189 REMARK 465 LYS A 190 REMARK 465 ARG A 191 REMARK 465 LEU A 192 REMARK 465 LYS A 193 REMARK 465 MET B 69 REMARK 465 ARG B 70 REMARK 465 LEU B 71 REMARK 465 ASN B 72 REMARK 465 SER B 73 REMARK 465 THR B 74 REMARK 465 GLY B 75 REMARK 465 GLU B 76 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 SER C 73 REMARK 465 THR C 74 REMARK 465 GLY C 75 REMARK 465 GLY C 165 REMARK 465 ASN C 166 REMARK 465 THR C 167 REMARK 465 GLU C 168 REMARK 465 SER C 169 REMARK 465 GLU C 170 REMARK 465 LEU C 171 REMARK 465 LYS C 172 REMARK 465 LYS C 173 REMARK 465 LEU C 174 REMARK 465 ALA C 175 REMARK 465 GLU C 176 REMARK 465 GLU C 177 REMARK 465 ASN C 178 REMARK 465 PRO C 179 REMARK 465 ASP C 180 REMARK 465 LEU C 181 REMARK 465 GLN C 182 REMARK 465 GLU C 183 REMARK 465 ALA C 184 REMARK 465 TYR C 185 REMARK 465 THR D 74 REMARK 465 GLY D 75 REMARK 465 GLY D 165 REMARK 465 ASN D 166 REMARK 465 THR D 167 REMARK 465 GLU D 168 REMARK 465 SER D 169 REMARK 465 GLU D 170 REMARK 465 LEU D 171 REMARK 465 LYS D 172 REMARK 465 LYS D 173 REMARK 465 LEU D 174 REMARK 465 ALA D 175 REMARK 465 GLU D 176 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 O ASP B 198 H ASP B 200 1.50 REMARK 500 O ASP B 198 N ASP B 200 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 NZ LYS B 203 O ASN C 270 4655 2.02 REMARK 500 OH TYR D 29 OH TYR D 29 4555 2.17 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 HIS A 33 43.59 -104.28 REMARK 500 PRO A 59 -94.76 -50.73 REMARK 500 GLU A 65 99.73 -52.00 REMARK 500 GLU A 89 137.00 68.38 REMARK 500 HIS A 199 -88.81 69.53 REMARK 500 ASN A 201 -135.28 72.46 REMARK 500 CYS A 240 78.80 -114.75 REMARK 500 HIS B 33 44.43 -105.06 REMARK 500 PRO B 59 171.06 -56.25 REMARK 500 GLU B 62 -45.34 -174.51 REMARK 500 TRP B 67 6.18 -69.07 REMARK 500 GLU B 89 142.76 65.77 REMARK 500 HIS B 199 -55.35 55.30 REMARK 500 ASN B 201 -87.02 22.42 REMARK 500 CYS B 240 79.66 -115.09 REMARK 500 HIS C 33 44.03 -102.11 REMARK 500 LEU C 60 -70.53 -173.68 REMARK 500 SER C 61 79.44 -107.81 REMARK 500 LEU C 71 1.54 -159.09 REMARK 500 GLU C 89 146.24 65.09 REMARK 500 HIS C 199 -71.65 43.81 REMARK 500 ASN C 201 -129.53 56.63 REMARK 500 CYS C 240 79.97 -116.70 REMARK 500 HIS D 33 46.30 -109.98 REMARK 500 LEU D 60 100.87 -49.87 REMARK 500 GLU D 62 -86.21 59.54 REMARK 500 HIS D 63 83.18 -154.97 REMARK 500 PHE D 68 -68.63 -125.31 REMARK 500 GLU D 89 138.68 64.12 REMARK 500 HIS D 199 -32.44 -33.15 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 GLU D 76 VAL D 77 134.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7Q6K RELATED DB: PDB REMARK 900 RELATED ID: 7Q6J RELATED DB: PDB DBREF 7YWD A 23 294 UNP Q8TB36 GDAP1_HUMAN 23 294 DBREF 7YWD B 23 294 UNP Q8TB36 GDAP1_HUMAN 23 294 DBREF 7YWD C 23 294 UNP Q8TB36 GDAP1_HUMAN 23 294 DBREF 7YWD D 23 294 UNP Q8TB36 GDAP1_HUMAN 23 294 SEQRES 1 A 272 GLU VAL LYS LEU ILE LEU TYR HIS TRP THR HIS SER PHE SEQRES 2 A 272 SER SER GLN LYS VAL ARG LEU VAL ILE ALA GLU LYS ALA SEQRES 3 A 272 LEU LYS CYS GLU GLU HIS ASP VAL SER LEU PRO LEU SER SEQRES 4 A 272 GLU HIS ASN GLU PRO TRP PHE MET ARG LEU ASN SER THR SEQRES 5 A 272 GLY GLU VAL PRO VAL LEU ILE HIS GLY GLU ASN ILE ILE SEQRES 6 A 272 CYS GLU ALA THR GLN ILE ILE ASP TYR LEU GLU GLN THR SEQRES 7 A 272 PHE LEU ASP GLU ARG THR PRO ARG LEU MET PRO ASP LYS SEQRES 8 A 272 GLU SER MET TYR TYR PRO ARG VAL GLN HIS TYR ARG GLU SEQRES 9 A 272 LEU LEU ASP SER LEU PRO MET ASP ALA TYR THR HIS GLY SEQRES 10 A 272 CYS ILE LEU HIS PRO GLU LEU THR VAL ASP SER MET ILE SEQRES 11 A 272 PRO ALA TYR ALA THR THR ARG ILE ARG SER GLN ILE GLY SEQRES 12 A 272 ASN THR GLU SER GLU LEU LYS LYS LEU ALA GLU GLU ASN SEQRES 13 A 272 PRO ASP LEU GLN GLU ALA TYR ILE ALA LYS GLN LYS ARG SEQRES 14 A 272 LEU LYS SER LYS LEU LEU ASP HIS ASP ASN VAL LYS TYR SEQRES 15 A 272 LEU LYS LYS ILE LEU ASP GLU LEU GLU LYS VAL LEU ASP SEQRES 16 A 272 GLN VAL GLU THR GLU LEU GLN ARG ARG ASN GLU GLU THR SEQRES 17 A 272 PRO GLU GLU GLY GLN GLN PRO TRP LEU CYS GLY GLU SER SEQRES 18 A 272 PHE THR LEU ALA ASP VAL SER LEU ALA VAL THR LEU HIS SEQRES 19 A 272 ARG LEU LYS PHE LEU GLY PHE ALA ARG ARG ASN TRP GLY SEQRES 20 A 272 ASN GLY LYS ARG PRO ASN LEU GLU THR TYR TYR GLU ARG SEQRES 21 A 272 VAL LEU LYS ARG LYS THR PHE ASN LYS VAL LEU GLY SEQRES 1 B 272 GLU VAL LYS LEU ILE LEU TYR HIS TRP THR HIS SER PHE SEQRES 2 B 272 SER SER GLN LYS VAL ARG LEU VAL ILE ALA GLU LYS ALA SEQRES 3 B 272 LEU LYS CYS GLU GLU HIS ASP VAL SER LEU PRO LEU SER SEQRES 4 B 272 GLU HIS ASN GLU PRO TRP PHE MET ARG LEU ASN SER THR SEQRES 5 B 272 GLY GLU VAL PRO VAL LEU ILE HIS GLY GLU ASN ILE ILE SEQRES 6 B 272 CYS GLU ALA THR GLN ILE ILE ASP TYR LEU GLU GLN THR SEQRES 7 B 272 PHE LEU ASP GLU ARG THR PRO ARG LEU MET PRO ASP LYS SEQRES 8 B 272 GLU SER MET TYR TYR PRO ARG VAL GLN HIS TYR ARG GLU SEQRES 9 B 272 LEU LEU ASP SER LEU PRO MET ASP ALA TYR THR HIS GLY SEQRES 10 B 272 CYS ILE LEU HIS PRO GLU LEU THR VAL ASP SER MET ILE SEQRES 11 B 272 PRO ALA TYR ALA THR THR ARG ILE ARG SER GLN ILE GLY SEQRES 12 B 272 ASN THR GLU SER GLU LEU LYS LYS LEU ALA GLU GLU ASN SEQRES 13 B 272 PRO ASP LEU GLN GLU ALA TYR ILE ALA LYS GLN LYS ARG SEQRES 14 B 272 LEU LYS SER LYS LEU LEU ASP HIS ASP ASN VAL LYS TYR SEQRES 15 B 272 LEU LYS LYS ILE LEU ASP GLU LEU GLU LYS VAL LEU ASP SEQRES 16 B 272 GLN VAL GLU THR GLU LEU GLN ARG ARG ASN GLU GLU THR SEQRES 17 B 272 PRO GLU GLU GLY GLN GLN PRO TRP LEU CYS GLY GLU SER SEQRES 18 B 272 PHE THR LEU ALA ASP VAL SER LEU ALA VAL THR LEU HIS SEQRES 19 B 272 ARG LEU LYS PHE LEU GLY PHE ALA ARG ARG ASN TRP GLY SEQRES 20 B 272 ASN GLY LYS ARG PRO ASN LEU GLU THR TYR TYR GLU ARG SEQRES 21 B 272 VAL LEU LYS ARG LYS THR PHE ASN LYS VAL LEU GLY SEQRES 1 C 272 GLU VAL LYS LEU ILE LEU TYR HIS TRP THR HIS SER PHE SEQRES 2 C 272 SER SER GLN LYS VAL ARG LEU VAL ILE ALA GLU LYS ALA SEQRES 3 C 272 LEU LYS CYS GLU GLU HIS ASP VAL SER LEU PRO LEU SER SEQRES 4 C 272 GLU HIS ASN GLU PRO TRP PHE MET ARG LEU ASN SER THR SEQRES 5 C 272 GLY GLU VAL PRO VAL LEU ILE HIS GLY GLU ASN ILE ILE SEQRES 6 C 272 CYS GLU ALA THR GLN ILE ILE ASP TYR LEU GLU GLN THR SEQRES 7 C 272 PHE LEU ASP GLU ARG THR PRO ARG LEU MET PRO ASP LYS SEQRES 8 C 272 GLU SER MET TYR TYR PRO ARG VAL GLN HIS TYR ARG GLU SEQRES 9 C 272 LEU LEU ASP SER LEU PRO MET ASP ALA TYR THR HIS GLY SEQRES 10 C 272 CYS ILE LEU HIS PRO GLU LEU THR VAL ASP SER MET ILE SEQRES 11 C 272 PRO ALA TYR ALA THR THR ARG ILE ARG SER GLN ILE GLY SEQRES 12 C 272 ASN THR GLU SER GLU LEU LYS LYS LEU ALA GLU GLU ASN SEQRES 13 C 272 PRO ASP LEU GLN GLU ALA TYR ILE ALA LYS GLN LYS ARG SEQRES 14 C 272 LEU LYS SER LYS LEU LEU ASP HIS ASP ASN VAL LYS TYR SEQRES 15 C 272 LEU LYS LYS ILE LEU ASP GLU LEU GLU LYS VAL LEU ASP SEQRES 16 C 272 GLN VAL GLU THR GLU LEU GLN ARG ARG ASN GLU GLU THR SEQRES 17 C 272 PRO GLU GLU GLY GLN GLN PRO TRP LEU CYS GLY GLU SER SEQRES 18 C 272 PHE THR LEU ALA ASP VAL SER LEU ALA VAL THR LEU HIS SEQRES 19 C 272 ARG LEU LYS PHE LEU GLY PHE ALA ARG ARG ASN TRP GLY SEQRES 20 C 272 ASN GLY LYS ARG PRO ASN LEU GLU THR TYR TYR GLU ARG SEQRES 21 C 272 VAL LEU LYS ARG LYS THR PHE ASN LYS VAL LEU GLY SEQRES 1 D 272 GLU VAL LYS LEU ILE LEU TYR HIS TRP THR HIS SER PHE SEQRES 2 D 272 SER SER GLN LYS VAL ARG LEU VAL ILE ALA GLU LYS ALA SEQRES 3 D 272 LEU LYS CYS GLU GLU HIS ASP VAL SER LEU PRO LEU SER SEQRES 4 D 272 GLU HIS ASN GLU PRO TRP PHE MET ARG LEU ASN SER THR SEQRES 5 D 272 GLY GLU VAL PRO VAL LEU ILE HIS GLY GLU ASN ILE ILE SEQRES 6 D 272 CYS GLU ALA THR GLN ILE ILE ASP TYR LEU GLU GLN THR SEQRES 7 D 272 PHE LEU ASP GLU ARG THR PRO ARG LEU MET PRO ASP LYS SEQRES 8 D 272 GLU SER MET TYR TYR PRO ARG VAL GLN HIS TYR ARG GLU SEQRES 9 D 272 LEU LEU ASP SER LEU PRO MET ASP ALA TYR THR HIS GLY SEQRES 10 D 272 CYS ILE LEU HIS PRO GLU LEU THR VAL ASP SER MET ILE SEQRES 11 D 272 PRO ALA TYR ALA THR THR ARG ILE ARG SER GLN ILE GLY SEQRES 12 D 272 ASN THR GLU SER GLU LEU LYS LYS LEU ALA GLU GLU ASN SEQRES 13 D 272 PRO ASP LEU GLN GLU ALA TYR ILE ALA LYS GLN LYS ARG SEQRES 14 D 272 LEU LYS SER LYS LEU LEU ASP HIS ASP ASN VAL LYS TYR SEQRES 15 D 272 LEU LYS LYS ILE LEU ASP GLU LEU GLU LYS VAL LEU ASP SEQRES 16 D 272 GLN VAL GLU THR GLU LEU GLN ARG ARG ASN GLU GLU THR SEQRES 17 D 272 PRO GLU GLU GLY GLN GLN PRO TRP LEU CYS GLY GLU SER SEQRES 18 D 272 PHE THR LEU ALA ASP VAL SER LEU ALA VAL THR LEU HIS SEQRES 19 D 272 ARG LEU LYS PHE LEU GLY PHE ALA ARG ARG ASN TRP GLY SEQRES 20 D 272 ASN GLY LYS ARG PRO ASN LEU GLU THR TYR TYR GLU ARG SEQRES 21 D 272 VAL LEU LYS ARG LYS THR PHE ASN LYS VAL LEU GLY HELIX 1 AA1 SER A 34 ALA A 48 1 15 HELIX 2 AA2 GLU A 89 PHE A 101 1 13 HELIX 3 AA3 MET A 116 SER A 130 1 15 HELIX 4 AA4 PRO A 132 HIS A 143 1 12 HELIX 5 AA5 PRO A 144 THR A 147 5 4 HELIX 6 AA6 PRO A 153 THR A 167 1 15 HELIX 7 AA7 LYS A 195 HIS A 199 1 5 HELIX 8 AA8 ASN A 201 THR A 230 1 30 HELIX 9 AA9 THR A 245 GLY A 262 1 18 HELIX 10 AB1 PHE A 263 TRP A 268 1 6 HELIX 11 AB2 ARG A 273 ARG A 286 1 14 HELIX 12 AB3 ARG A 286 LEU A 293 1 8 HELIX 13 AB4 SER B 34 ALA B 48 1 15 HELIX 14 AB5 PRO B 59 ASN B 64 1 6 HELIX 15 AB6 GLU B 89 PHE B 101 1 13 HELIX 16 AB7 TYR B 117 SER B 130 1 14 HELIX 17 AB8 PRO B 132 HIS B 143 1 12 HELIX 18 AB9 PRO B 144 THR B 147 5 4 HELIX 19 AC1 PRO B 153 GLU B 168 1 16 HELIX 20 AC2 GLN B 189 HIS B 199 1 11 HELIX 21 AC3 ASP B 200 THR B 230 1 31 HELIX 22 AC4 THR B 245 GLY B 262 1 18 HELIX 23 AC5 PHE B 263 GLY B 269 1 7 HELIX 24 AC6 ARG B 273 ARG B 286 1 14 HELIX 25 AC7 ARG B 286 LEU B 293 1 8 HELIX 26 AC8 SER C 34 ALA C 48 1 15 HELIX 27 AC9 GLU C 89 PHE C 101 1 13 HELIX 28 AD1 MET C 116 SER C 130 1 15 HELIX 29 AD2 PRO C 132 HIS C 143 1 12 HELIX 30 AD3 PRO C 144 THR C 147 5 4 HELIX 31 AD4 PRO C 153 ILE C 164 1 12 HELIX 32 AD5 ALA C 187 HIS C 199 1 13 HELIX 33 AD6 ASN C 201 THR C 230 1 30 HELIX 34 AD7 THR C 245 GLY C 262 1 18 HELIX 35 AD8 PHE C 263 TRP C 268 1 6 HELIX 36 AD9 ARG C 273 ARG C 286 1 14 HELIX 37 AE1 ARG C 286 LEU C 293 1 8 HELIX 38 AE2 SER D 34 ALA D 48 1 15 HELIX 39 AE3 GLU D 89 PHE D 101 1 13 HELIX 40 AE4 TYR D 117 SER D 130 1 14 HELIX 41 AE5 PRO D 132 HIS D 143 1 12 HELIX 42 AE6 PRO D 144 THR D 147 5 4 HELIX 43 AE7 PRO D 153 ILE D 164 1 12 HELIX 44 AE8 ASN D 178 HIS D 199 1 22 HELIX 45 AE9 ASP D 200 THR D 230 1 31 HELIX 46 AF1 THR D 245 GLY D 262 1 18 HELIX 47 AF2 PHE D 263 TRP D 268 1 6 HELIX 48 AF3 ARG D 273 ARG D 286 1 14 HELIX 49 AF4 ARG D 286 LEU D 293 1 8 SHEET 1 AA1 4 CYS A 51 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 VAL A 79 N TYR A 29 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 VAL B 79 N TYR B 29 SHEET 4 AA2 4 ASN B 85 CYS B 88 -1 O ILE B 87 N LEU B 80 SHEET 1 AA3 4 CYS C 51 ASP C 55 0 SHEET 2 AA3 4 LEU C 26 HIS C 30 1 N LEU C 28 O HIS C 54 SHEET 3 AA3 4 VAL C 79 HIS C 82 -1 O VAL C 79 N TYR C 29 SHEET 4 AA3 4 ASN C 85 CYS C 88 -1 O ILE C 87 N LEU C 80 SHEET 1 AA4 4 CYS D 51 ASP D 55 0 SHEET 2 AA4 4 LEU D 26 HIS D 30 1 N LEU D 26 O GLU D 52 SHEET 3 AA4 4 VAL D 79 HIS D 82 -1 O ILE D 81 N ILE D 27 SHEET 4 AA4 4 ASN D 85 CYS D 88 -1 O ILE D 87 N LEU D 80 SSBOND 1 CYS A 88 CYS A 88 1555 6554 2.04 SSBOND 2 CYS D 88 CYS D 88 1555 4555 2.03 CRYST1 126.770 126.770 177.120 90.00 90.00 120.00 P 31 2 1 24 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 0.007888 0.004554 0.000000 0.00000 SCALE2 0.000000 0.009109 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005646 0.00000 MTRIX1 1 0.053936 0.993260 -0.102593 63.96085 1 MTRIX2 1 0.958194 -0.022571 0.285227 -55.88603 1 MTRIX3 1 0.280989 -0.113688 -0.952954 -79.77461 1 MTRIX1 2 -0.870892 0.474929 0.126452 78.79502 1 MTRIX2 2 -0.488794 -0.810148 -0.323636 -88.53288 1 MTRIX3 2 -0.051259 -0.343661 0.937694 29.59973 1 MTRIX1 3 0.438605 0.783633 0.439937 59.69461 1 MTRIX2 3 -0.826949 0.543578 -0.143797 55.81799 1 MTRIX3 3 -0.351824 -0.300735 0.886441 46.32093 1