PDB Short entry for 4PED HEADER TRANSFERASE 23-APR-14 4PED TITLE MITOCHONDRIAL ADCK3 EMPLOYS AN ATYPICAL PROTEIN KINASE-LIKE FOLD TO TITLE 2 ENABLE COENZYME Q BIOSYNTHES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAPERONE ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 204-595; COMPND 5 SYNONYM: CHAPERONE-ABC1-LIKE,AARF DOMAIN-CONTAINING PROTEIN KINASE 3; COMPND 6 EC: 2.7.11.-; 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: ADCK3, CABC1, PP265; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN KINASE-LIKE, COENZYME Q BIOSYNTHESIS, MITOCHONDRIAL, MEMBRANE KEYWDS 2 ASSOCIATED, STRUCTURAL GENOMICS, PSI-BIOLOGY, MITOCHONDRIAL PROTEIN KEYWDS 3 PARTNERSHIP, MPP, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.BINGMAN,R.SMITH,S.JOSHI,J.A.STEFELY,A.G.REIDENBACH,A.ULBRICH, AUTHOR 2 O.ORUGANTY,B.J.FLOYD,A.JOCHEM,J.M.SAUNDERS,I.E.JOHNSON,R.L.WROBEL, AUTHOR 3 G.E.BARBER,D.LEE,S.LI,N.KANNAN,J.J.COON,D.J.PAGLIARINI,MITOCHONDRIAL AUTHOR 4 PROTEIN PARTNERSHIP (MPP) REVDAT 6 27-DEC-23 4PED 1 REMARK REVDAT 5 25-DEC-19 4PED 1 REMARK REVDAT 4 06-SEP-17 4PED 1 SOURCE JRNL REMARK REVDAT 3 21-JAN-15 4PED 1 JRNL REVDAT 2 14-JAN-15 4PED 1 JRNL REVDAT 1 19-NOV-14 4PED 0 JRNL AUTH J.A.STEFELY,A.G.REIDENBACH,A.ULBRICH,K.ORUGANTY,B.J.FLOYD, JRNL AUTH 2 A.JOCHEM,J.M.SAUNDERS,I.E.JOHNSON,C.E.MINOGUE,R.L.WROBEL, JRNL AUTH 3 G.E.BARBER,D.LEE,S.LI,N.KANNAN,J.J.COON,C.A.BINGMAN, JRNL AUTH 4 D.J.PAGLIARINI JRNL TITL MITOCHONDRIAL ADCK3 EMPLOYS AN ATYPICAL PROTEIN KINASE-LIKE JRNL TITL 2 FOLD TO ENABLE COENZYME Q BIOSYNTHESIS. JRNL REF MOL.CELL V. 57 83 2015 JRNL REFN ISSN 1097-2765 JRNL PMID 25498144 JRNL DOI 10.1016/J.MOLCEL.2014.11.002 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.1 REMARK 3 NUMBER OF REFLECTIONS : 69420 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 3478 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 36.6427 - 4.7880 1.00 3262 197 0.1606 0.1806 REMARK 3 2 4.7880 - 3.8016 0.99 3298 138 0.1264 0.2154 REMARK 3 3 3.8016 - 3.3215 0.99 3280 163 0.1491 0.1930 REMARK 3 4 3.3215 - 3.0179 0.99 3232 175 0.1727 0.1997 REMARK 3 5 3.0179 - 2.8017 0.99 3274 185 0.1766 0.1941 REMARK 3 6 2.8017 - 2.6366 0.98 3217 136 0.1702 0.2223 REMARK 3 7 2.6366 - 2.5046 0.98 3267 176 0.1656 0.2248 REMARK 3 8 2.5046 - 2.3956 0.98 3186 173 0.1560 0.2083 REMARK 3 9 2.3956 - 2.3033 0.98 3286 164 0.1595 0.1930 REMARK 3 10 2.3033 - 2.2239 0.98 3210 163 0.1582 0.2500 REMARK 3 11 2.2239 - 2.1543 0.97 3236 133 0.1536 0.2009 REMARK 3 12 2.1543 - 2.0928 0.97 3177 178 0.1646 0.2329 REMARK 3 13 2.0928 - 2.0377 0.97 3182 187 0.1721 0.2270 REMARK 3 14 2.0377 - 1.9880 0.92 2987 194 0.1724 0.2190 REMARK 3 15 1.9880 - 1.9428 0.87 2830 166 0.1808 0.2472 REMARK 3 16 1.9428 - 1.9014 0.81 2647 159 0.1775 0.2360 REMARK 3 17 1.9014 - 1.8634 0.75 2459 135 0.1884 0.1909 REMARK 3 18 1.8634 - 1.8282 0.69 2299 110 0.1874 0.2424 REMARK 3 19 1.8282 - 1.7956 0.62 2052 101 0.1930 0.2264 REMARK 3 20 1.7956 - 1.7652 0.57 1868 100 0.2016 0.2349 REMARK 3 21 1.7652 - 1.7367 0.53 1770 75 0.2151 0.2073 REMARK 3 22 1.7367 - 1.7100 0.50 1654 89 0.2292 0.2513 REMARK 3 23 1.7100 - 1.6848 0.42 1362 71 0.2482 0.2448 REMARK 3 24 1.6848 - 1.6611 0.33 1104 69 0.2510 0.2754 REMARK 3 25 1.6611 - 1.6400 0.25 803 41 0.2564 0.2832 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.550 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 : 0.012 3308 REMARK 3 ANGLE : 1.433 4488 REMARK 3 CHIRALITY : 0.060 484 REMARK 3 PLANARITY : 0.007 586 REMARK 3 DIHEDRAL : 15.844 1281 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 258 THROUGH 306 ) REMARK 3 ORIGIN FOR THE GROUP (A): 62.3008 12.4400 28.9541 REMARK 3 T TENSOR REMARK 3 T11: 0.0665 T22: 0.0931 REMARK 3 T33: 0.0789 T12: 0.0089 REMARK 3 T13: 0.0042 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 1.0691 L22: 1.9647 REMARK 3 L33: 1.4901 L12: 0.0070 REMARK 3 L13: 0.1527 L23: -0.4492 REMARK 3 S TENSOR REMARK 3 S11: -0.0160 S12: -0.1225 S13: 0.0259 REMARK 3 S21: 0.0224 S22: 0.0220 S23: -0.1554 REMARK 3 S31: 0.0266 S32: 0.0082 S33: -0.0086 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 307 THROUGH 407 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.0634 -0.6137 27.9839 REMARK 3 T TENSOR REMARK 3 T11: 0.1274 T22: 0.0902 REMARK 3 T33: 0.1495 T12: -0.0214 REMARK 3 T13: -0.0343 T23: 0.0362 REMARK 3 L TENSOR REMARK 3 L11: 0.9602 L22: 0.4995 REMARK 3 L33: 0.7657 L12: -0.3693 REMARK 3 L13: 0.1775 L23: 0.2972 REMARK 3 S TENSOR REMARK 3 S11: 0.0891 S12: -0.2136 S13: -0.2223 REMARK 3 S21: 0.0811 S22: 0.0482 S23: -0.0547 REMARK 3 S31: 0.1385 S32: -0.0679 S33: -0.0197 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 408 THROUGH 505 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.1148 3.5794 9.0581 REMARK 3 T TENSOR REMARK 3 T11: 0.0717 T22: 0.0737 REMARK 3 T33: 0.0604 T12: 0.0107 REMARK 3 T13: 0.0075 T23: -0.0124 REMARK 3 L TENSOR REMARK 3 L11: 0.6050 L22: 0.9905 REMARK 3 L33: 0.7403 L12: 0.2134 REMARK 3 L13: 0.2272 L23: -0.5464 REMARK 3 S TENSOR REMARK 3 S11: 0.1237 S12: 0.0339 S13: -0.0876 REMARK 3 S21: -0.0356 S22: -0.0613 S23: -0.0215 REMARK 3 S31: 0.0905 S32: 0.0029 S33: -0.0564 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 506 THROUGH 644 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.6005 21.2859 11.9981 REMARK 3 T TENSOR REMARK 3 T11: 0.0703 T22: 0.0859 REMARK 3 T33: 0.0604 T12: 0.0120 REMARK 3 T13: 0.0055 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 1.0643 L22: 0.6765 REMARK 3 L33: 0.5632 L12: -0.7203 REMARK 3 L13: -0.1238 L23: -0.1861 REMARK 3 S TENSOR REMARK 3 S11: 0.0097 S12: 0.0130 S13: 0.0393 REMARK 3 S21: -0.0267 S22: 0.0025 S23: 0.0260 REMARK 3 S31: -0.0238 S32: -0.1187 S33: 0.0015 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4PED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000201236. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69420 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.89300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: MONOCLINIC RHOMB-SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SEEDED MICROBATCH EXPERIMENT, 5 MG/ML REMARK 280 PROTEIN 12.5% PEG 3350, 50 MM HEPES PH 7.5, 5 MM MGCL2, 150 MM REMARK 280 AM2SO4, 0.15 MM TCEP, 5 MICROLITER SITTING DROP IN BRIDGE OF VDX REMARK 280 PLATE, EQUILIBRATED AGAINST 12.5% PEG 3350, 50 MM HEPES PH 7.5, REMARK 280 150 MM AM2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 74.33550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.27850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.33550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.27850 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 255 REMARK 465 SER A 256 REMARK 465 GLU A 257 REMARK 465 ALA A 645 REMARK 465 GLN A 646 REMARK 465 GLN A 647 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 HE21 GLN A 343 HH TYR A 361 0.97 REMARK 500 OE2 GLU A 466 HE2 HIS A 501 1.37 REMARK 500 O LYS A 327 H LYS A 350 1.44 REMARK 500 OD1 ASP A 520 HH TYR A 640 1.59 REMARK 500 O PRO A 489 O HOH A 1008 1.94 REMARK 500 OE2 GLU A 604 O HOH A 948 1.98 REMARK 500 O HOH A 811 O HOH A 910 2.03 REMARK 500 O HOH A 828 O HOH A 910 2.08 REMARK 500 OE2 GLU A 635 O HOH A 801 2.09 REMARK 500 OG SER A 621 O HOH A 979 2.17 REMARK 500 O HOH A 905 O HOH A 1037 2.18 REMARK 500 OD1 ASP A 420 O HOH A 1052 2.18 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 OE1 GLU A 333 HH22 ARG A 348 2656 1.51 REMARK 500 O HOH A 863 O HOH A 888 2656 2.07 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 348 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ASP A 286 -168.24 -125.22 REMARK 500 ASN A 323 103.86 56.78 REMARK 500 TRP A 324 -40.26 -142.54 REMARK 500 SER A 340 -98.93 41.16 REMARK 500 ASN A 490 74.91 76.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MPP-GO.120289 RELATED DB: TARGETTRACK DBREF 4PED A 256 647 UNP Q8NI60 ADCK3_HUMAN 204 595 SEQADV 4PED SER A 255 UNP Q8NI60 EXPRESSION TAG SEQRES 1 A 393 SER SER GLU ALA ASN ALA GLU ARG ILE VAL ARG THR LEU SEQRES 2 A 393 CYS LYS VAL ARG GLY ALA ALA LEU LYS LEU GLY GLN MSE SEQRES 3 A 393 LEU SER ILE GLN ASP ASP ALA PHE ILE ASN PRO HIS LEU SEQRES 4 A 393 ALA LYS ILE PHE GLU ARG VAL ARG GLN SER ALA ASP PHE SEQRES 5 A 393 MSE PRO LEU LYS GLN MSE MSE LYS THR LEU ASN ASN ASP SEQRES 6 A 393 LEU GLY PRO ASN TRP ARG ASP LYS LEU GLU TYR PHE GLU SEQRES 7 A 393 GLU ARG PRO PHE ALA ALA ALA SER ILE GLY GLN VAL HIS SEQRES 8 A 393 LEU ALA ARG MSE LYS GLY GLY ARG GLU VAL ALA MSE LYS SEQRES 9 A 393 ILE GLN TYR PRO GLY VAL ALA GLN SER ILE ASN SER ASP SEQRES 10 A 393 VAL ASN ASN LEU MSE ALA VAL LEU ASN MSE SER ASN MSE SEQRES 11 A 393 LEU PRO GLU GLY LEU PHE PRO GLU HIS LEU ILE ASP VAL SEQRES 12 A 393 LEU ARG ARG GLU LEU ALA LEU GLU CYS ASP TYR GLN ARG SEQRES 13 A 393 GLU ALA ALA CYS ALA ARG LYS PHE ARG ASP LEU LEU LYS SEQRES 14 A 393 GLY HIS PRO PHE PHE TYR VAL PRO GLU ILE VAL ASP GLU SEQRES 15 A 393 LEU CYS SER PRO HIS VAL LEU THR THR GLU LEU VAL SER SEQRES 16 A 393 GLY PHE PRO LEU ASP GLN ALA GLU GLY LEU SER GLN GLU SEQRES 17 A 393 ILE ARG ASN GLU ILE CYS TYR ASN ILE LEU VAL LEU CYS SEQRES 18 A 393 LEU ARG GLU LEU PHE GLU PHE HIS PHE MSE GLN THR ASP SEQRES 19 A 393 PRO ASN TRP SER ASN PHE PHE TYR ASP PRO GLN GLN HIS SEQRES 20 A 393 LYS VAL ALA LEU LEU ASP PHE GLY ALA THR ARG GLU TYR SEQRES 21 A 393 ASP ARG SER PHE THR ASP LEU TYR ILE GLN ILE ILE ARG SEQRES 22 A 393 ALA ALA ALA ASP ARG ASP ARG GLU THR VAL ARG ALA LYS SEQRES 23 A 393 SER ILE GLU MSE LYS PHE LEU THR GLY TYR GLU VAL LYS SEQRES 24 A 393 VAL MSE GLU ASP ALA HIS LEU ASP ALA ILE LEU ILE LEU SEQRES 25 A 393 GLY GLU ALA PHE ALA SER ASP GLU PRO PHE ASP PHE GLY SEQRES 26 A 393 THR GLN SER THR THR GLU LYS ILE HIS ASN LEU ILE PRO SEQRES 27 A 393 VAL MSE LEU ARG HIS ARG LEU VAL PRO PRO PRO GLU GLU SEQRES 28 A 393 THR TYR SER LEU HIS ARG LYS MSE GLY GLY SER PHE LEU SEQRES 29 A 393 ILE CYS SER LYS LEU LYS ALA ARG PHE PRO CYS LYS ALA SEQRES 30 A 393 MSE PHE GLU GLU ALA TYR SER ASN TYR CYS LYS ARG GLN SEQRES 31 A 393 ALA GLN GLN MODRES 4PED MSE A 280 MET MODIFIED RESIDUE MODRES 4PED MSE A 307 MET MODIFIED RESIDUE MODRES 4PED MSE A 312 MET MODIFIED RESIDUE MODRES 4PED MSE A 313 MET MODIFIED RESIDUE MODRES 4PED MSE A 349 MET MODIFIED RESIDUE MODRES 4PED MSE A 357 MET MODIFIED RESIDUE MODRES 4PED MSE A 376 MET MODIFIED RESIDUE MODRES 4PED MSE A 381 MET MODIFIED RESIDUE MODRES 4PED MSE A 384 MET MODIFIED RESIDUE MODRES 4PED MSE A 485 MET MODIFIED RESIDUE MODRES 4PED MSE A 544 MET MODIFIED RESIDUE MODRES 4PED MSE A 555 MET MODIFIED RESIDUE MODRES 4PED MSE A 594 MET MODIFIED RESIDUE MODRES 4PED MSE A 613 MET MODIFIED RESIDUE MODRES 4PED MSE A 632 MET MODIFIED RESIDUE HET MSE A 280 10 HET MSE A 307 15 HET MSE A 312 17 HET MSE A 313 17 HET MSE A 349 10 HET MSE A 357 10 HET MSE A 376 20 HET MSE A 381 10 HET MSE A 384 9 HET MSE A 485 15 HET MSE A 544 10 HET MSE A 555 15 HET MSE A 594 10 HET MSE A 613 15 HET MSE A 632 15 HET SO4 A 701 5 HET SO4 A 702 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 15(C5 H11 N O2 SE) FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *267(H2 O) HELIX 1 AA1 ASN A 259 VAL A 270 1 12 HELIX 2 AA2 VAL A 270 SER A 282 1 13 HELIX 3 AA3 ASN A 290 SER A 303 1 14 HELIX 4 AA4 ALA A 304 MSE A 307 5 4 HELIX 5 AA5 PRO A 308 GLY A 321 1 14 HELIX 6 AA6 TRP A 324 ASP A 326 5 3 HELIX 7 AA7 VAL A 364 GLN A 366 5 3 HELIX 8 AA8 SER A 367 ASN A 383 1 17 HELIX 9 AA9 PHE A 390 HIS A 393 5 4 HELIX 10 AB1 LEU A 394 CYS A 406 1 13 HELIX 11 AB2 ASP A 407 LEU A 422 1 16 HELIX 12 AB3 VAL A 434 CYS A 438 5 5 HELIX 13 AB4 ASP A 454 ALA A 456 5 3 HELIX 14 AB5 SER A 460 GLU A 481 1 22 HELIX 15 AB6 ASN A 490 SER A 492 5 3 HELIX 16 AB7 ASP A 515 ASP A 531 1 17 HELIX 17 AB8 ASP A 533 MSE A 544 1 12 HELIX 18 AB9 VAL A 552 SER A 572 1 21 HELIX 19 AC1 THR A 580 ASN A 589 1 10 HELIX 20 AC2 LEU A 590 LEU A 595 5 6 HELIX 21 AC3 PRO A 603 LEU A 623 1 21 HELIX 22 AC4 CYS A 629 GLN A 644 1 16 SHEET 1 AA1 3 LEU A 328 PHE A 331 0 SHEET 2 AA1 3 GLY A 342 MSE A 349 -1 O ARG A 348 N TYR A 330 SHEET 3 AA1 3 ALA A 337 ALA A 339 -1 N ALA A 337 O VAL A 344 SHEET 1 AA2 4 LEU A 328 PHE A 331 0 SHEET 2 AA2 4 GLY A 342 MSE A 349 -1 O ARG A 348 N TYR A 330 SHEET 3 AA2 4 GLU A 354 GLN A 360 -1 O MSE A 357 N HIS A 345 SHEET 4 AA2 4 VAL A 442 GLU A 446 -1 O THR A 445 N ALA A 356 SHEET 1 AA3 4 PHE A 428 TYR A 429 0 SHEET 2 AA3 4 LYS A 502 LEU A 505 1 O LEU A 505 N TYR A 429 SHEET 3 AA3 4 PHE A 494 ASP A 497 -1 N ASP A 497 O LYS A 502 SHEET 4 AA3 4 PHE A 451 PRO A 452 -1 N PHE A 451 O TYR A 496 SHEET 1 AA4 2 PHE A 484 GLN A 486 0 SHEET 2 AA4 2 THR A 511 GLU A 513 -1 O ARG A 512 N MSE A 485 SHEET 1 AA5 2 PHE A 576 ASP A 577 0 SHEET 2 AA5 2 ARG A 626 PHE A 627 -1 O PHE A 627 N PHE A 576 LINK C GLN A 279 N MSE A 280 1555 1555 1.32 LINK C MSE A 280 N LEU A 281 1555 1555 1.34 LINK C PHE A 306 N MSE A 307 1555 1555 1.33 LINK C MSE A 307 N PRO A 308 1555 1555 1.34 LINK C GLN A 311 N MSE A 312 1555 1555 1.34 LINK C MSE A 312 N MSE A 313 1555 1555 1.33 LINK C MSE A 313 N LYS A 314 1555 1555 1.34 LINK C ARG A 348 N MSE A 349 1555 1555 1.33 LINK C MSE A 349 N LYS A 350 1555 1555 1.34 LINK C ALA A 356 N MSE A 357 1555 1555 1.33 LINK C MSE A 357 N LYS A 358 1555 1555 1.33 LINK C LEU A 375 N AMSE A 376 1555 1555 1.33 LINK C LEU A 375 N BMSE A 376 1555 1555 1.33 LINK C AMSE A 376 N ALA A 377 1555 1555 1.33 LINK C BMSE A 376 N ALA A 377 1555 1555 1.32 LINK C ASN A 380 N MSE A 381 1555 1555 1.33 LINK C MSE A 381 N SER A 382 1555 1555 1.33 LINK C ASN A 383 N MSE A 384 1555 1555 1.33 LINK C MSE A 384 N LEU A 385 1555 1555 1.34 LINK C PHE A 484 N MSE A 485 1555 1555 1.33 LINK C MSE A 485 N GLN A 486 1555 1555 1.32 LINK C GLU A 543 N MSE A 544 1555 1555 1.34 LINK C MSE A 544 N LYS A 545 1555 1555 1.33 LINK C VAL A 554 N MSE A 555 1555 1555 1.33 LINK C MSE A 555 N GLU A 556 1555 1555 1.33 LINK C VAL A 593 N MSE A 594 1555 1555 1.33 LINK C MSE A 594 N LEU A 595 1555 1555 1.33 LINK C LYS A 612 N MSE A 613 1555 1555 1.33 LINK C MSE A 613 N GLY A 614 1555 1555 1.33 LINK C ALA A 631 N MSE A 632 1555 1555 1.34 LINK C MSE A 632 N PHE A 633 1555 1555 1.34 SITE 1 AC1 6 ARG A 410 THR A 548 ARG A 596 ARG A 598 SITE 2 AC1 6 LEU A 599 HOH A 846 SITE 1 AC2 6 ASN A 259 LEU A 459 SER A 460 GLN A 461 SITE 2 AC2 6 ARG A 464 HOH A 841 CRYST1 148.671 54.557 45.009 90.00 94.00 90.00 C 1 2 1 4 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 0.006726 0.000000 0.000471 0.00000 SCALE2 0.000000 0.018329 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022272 0.00000