HEADER SUGAR BINDING PROTEIN, TRANSLOCASE 07-JUN-19 6K7E TITLE CRYSTAL STRUCTURE OF MBPAPO-TIM21 FUSION PROTEIN WITH A 17-RESIDUE TITLE 2 HELICAL LINKER COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALTOSE/MALTODEXTRIN-BINDING PERIPLASMIC PROTEIN, COMPND 3 MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM21; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: MMBP,MALTODEXTRIN-BINDING PROTEIN,MALTOSE-BINDING PROTEIN, COMPND 6 MBP; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: MBPAPO-TIM21 FUSION PROTEIN WITH A 17-RESIDUE HELICAL COMPND 10 LINKER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12), SACCHAROMYCES SOURCE 3 CEREVISIAE (STRAIN ATCC 204508 / S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 83333, 559292; SOURCE 6 GENE: MALE, B4034, JW3994, TIM21, YGR033C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS MBP, TIM21, FUSION PROTEIN, HELICAL LINKER, TRANSLOCASE, SUGAR KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.BALA,A.SHIMADA,D.KOHDA REVDAT 3 22-NOV-23 6K7E 1 REMARK REVDAT 2 01-APR-20 6K7E 1 JRNL REVDAT 1 18-SEP-19 6K7E 0 JRNL AUTH S.BALA,S.SHINYA,A.SRIVASTAVA,M.ISHIKAWA,A.SHIMADA, JRNL AUTH 2 N.KOBAYASHI,C.KOJIMA,F.TAMA,O.MIYASHITA,D.KOHDA JRNL TITL CRYSTAL CONTACT-FREE CONFORMATION OF AN INTRINSICALLY JRNL TITL 2 FLEXIBLE LOOP IN PROTEIN CRYSTAL: TIM21 AS THE CASE STUDY. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1864 29418 2020 JRNL REF 2 SUBJ JRNL REFN ISSN 1872-8006 JRNL PMID 31449839 JRNL DOI 10.1016/J.BBAGEN.2019.129418 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 92352 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) : 0.166 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 4494 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 39.2145 - 4.7640 0.97 2852 144 0.1713 0.1950 REMARK 3 2 4.7640 - 3.7823 1.00 2944 151 0.1379 0.1436 REMARK 3 3 3.7823 - 3.3045 1.00 2941 154 0.1530 0.1643 REMARK 3 4 3.3045 - 3.0025 1.00 2927 134 0.1587 0.1609 REMARK 3 5 3.0025 - 2.7873 1.00 2950 146 0.1685 0.1896 REMARK 3 6 2.7873 - 2.6230 1.00 2953 120 0.1690 0.1938 REMARK 3 7 2.6230 - 2.4917 1.00 2946 132 0.1658 0.2090 REMARK 3 8 2.4917 - 2.3832 1.00 2950 151 0.1699 0.1966 REMARK 3 9 2.3832 - 2.2915 1.00 2924 143 0.1671 0.2149 REMARK 3 10 2.2915 - 2.2124 1.00 2963 126 0.1681 0.2147 REMARK 3 11 2.2124 - 2.1433 1.00 2988 134 0.1624 0.2011 REMARK 3 12 2.1433 - 2.0820 1.00 2894 153 0.1588 0.2016 REMARK 3 13 2.0820 - 2.0272 1.00 2892 162 0.1615 0.1902 REMARK 3 14 2.0272 - 1.9777 1.00 2925 170 0.1655 0.1876 REMARK 3 15 1.9777 - 1.9328 1.00 2924 156 0.1733 0.1950 REMARK 3 16 1.9328 - 1.8917 1.00 2942 170 0.1668 0.2231 REMARK 3 17 1.8917 - 1.8538 1.00 2904 173 0.1709 0.1947 REMARK 3 18 1.8538 - 1.8188 1.00 2945 138 0.1748 0.2162 REMARK 3 19 1.8188 - 1.7864 1.00 2945 164 0.1875 0.2203 REMARK 3 20 1.7864 - 1.7561 1.00 2909 155 0.1963 0.2631 REMARK 3 21 1.7561 - 1.7277 1.00 2896 145 0.2007 0.2245 REMARK 3 22 1.7277 - 1.7012 1.00 2938 179 0.1821 0.2349 REMARK 3 23 1.7012 - 1.6761 1.00 2922 174 0.1898 0.2292 REMARK 3 24 1.6761 - 1.6525 1.00 2927 132 0.1880 0.2411 REMARK 3 25 1.6525 - 1.6302 1.00 2948 154 0.1945 0.2135 REMARK 3 26 1.6302 - 1.6090 1.00 2904 143 0.2006 0.2201 REMARK 3 27 1.6090 - 1.5889 1.00 2972 143 0.2231 0.2361 REMARK 3 28 1.5889 - 1.5698 1.00 2912 144 0.2373 0.3088 REMARK 3 29 1.5698 - 1.5515 1.00 2929 133 0.2590 0.2739 REMARK 3 30 1.5515 - 1.5341 0.99 2892 171 0.2785 0.3327 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.10 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 : 0.019 4000 REMARK 3 ANGLE : 1.719 5413 REMARK 3 CHIRALITY : 0.129 587 REMARK 3 PLANARITY : 0.009 700 REMARK 3 DIHEDRAL : 13.830 1491 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 353 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.9581 21.9158 -20.0450 REMARK 3 T TENSOR REMARK 3 T11: 0.0760 T22: 0.0684 REMARK 3 T33: 0.0666 T12: 0.0157 REMARK 3 T13: 0.0321 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.8288 L22: 0.3722 REMARK 3 L33: 0.6012 L12: -0.2498 REMARK 3 L13: 0.3448 L23: 0.0102 REMARK 3 S TENSOR REMARK 3 S11: -0.0549 S12: -0.0718 S13: -0.0226 REMARK 3 S21: 0.0230 S22: 0.0466 S23: 0.0725 REMARK 3 S31: -0.0824 S32: -0.0741 S33: 0.0047 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 354 THROUGH 399 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.3149 49.3169 -21.7278 REMARK 3 T TENSOR REMARK 3 T11: 0.2359 T22: 0.1197 REMARK 3 T33: 0.1842 T12: 0.0219 REMARK 3 T13: 0.0008 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.0314 L22: 0.0132 REMARK 3 L33: -0.0853 L12: -0.1296 REMARK 3 L13: 0.0606 L23: -0.0543 REMARK 3 S TENSOR REMARK 3 S11: -0.0293 S12: 0.0871 S13: 0.2125 REMARK 3 S21: -0.0554 S22: -0.0192 S23: -0.1952 REMARK 3 S31: -0.1025 S32: -0.0111 S33: -0.0010 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 400 THROUGH 500 ) REMARK 3 ORIGIN FOR THE GROUP (A): -55.6576 57.4005 -22.8245 REMARK 3 T TENSOR REMARK 3 T11: 0.1613 T22: 0.1160 REMARK 3 T33: 0.1100 T12: 0.0547 REMARK 3 T13: -0.0400 T23: -0.0220 REMARK 3 L TENSOR REMARK 3 L11: 0.6178 L22: 0.3523 REMARK 3 L33: 0.3239 L12: 0.1771 REMARK 3 L13: -0.1072 L23: 0.0282 REMARK 3 S TENSOR REMARK 3 S11: -0.0256 S12: 0.1045 S13: -0.0204 REMARK 3 S21: -0.0564 S22: -0.0498 S23: 0.2122 REMARK 3 S31: 0.0508 S32: -0.0316 S33: -0.0034 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 6K7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-17 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 : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 714 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 714 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.8_1069 REMARK 200 STARTING MODEL: 1PEB, 2CIU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M CACL2, 0.1M HEPES, PH 7.0, 20% REMARK 280 PEG 6000 (W/V), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 78.40350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.26628 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.46200 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 78.40350 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 45.26628 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.46200 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 78.40350 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 45.26628 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.46200 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.53256 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 44.92400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 90.53256 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 44.92400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 90.53256 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 44.92400 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 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLU A 501 REMARK 465 HIS A 502 REMARK 465 HIS A 503 REMARK 465 HIS A 504 REMARK 465 HIS A 505 REMARK 465 HIS A 506 REMARK 465 HIS A 507 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 HOH A 665 O HOH A 1098 1.80 REMARK 500 O HOH A 1106 O HOH A 1145 1.82 REMARK 500 OE2 GLU A 139 O HOH A 601 1.86 REMARK 500 O HOH A 735 O HOH A 996 1.87 REMARK 500 O HOH A 1135 O HOH A 1212 1.90 REMARK 500 O HOH A 1198 O HOH A 1244 1.90 REMARK 500 OG SER A 212 O HOH A 602 1.92 REMARK 500 O HOH A 1046 O HOH A 1200 1.92 REMARK 500 O HOH A 651 O HOH A 1283 1.93 REMARK 500 O HOH A 723 O HOH A 1249 1.93 REMARK 500 O HOH A 1029 O HOH A 1250 1.97 REMARK 500 O HOH A 1056 O HOH A 1249 1.98 REMARK 500 O HOH A 987 O HOH A 1338 2.00 REMARK 500 O HOH A 643 O HOH A 794 2.03 REMARK 500 NZ LYS A 443 O HOH A 603 2.04 REMARK 500 O HOH A 1005 O HOH A 1240 2.05 REMARK 500 O HOH A 1242 O HOH A 1351 2.05 REMARK 500 O HOH A 1191 O HOH A 1354 2.06 REMARK 500 O HOH A 975 O HOH A 1163 2.06 REMARK 500 O HOH A 717 O HOH A 1034 2.08 REMARK 500 O GLY A 33 O HOH A 604 2.08 REMARK 500 O HOH A 1022 O HOH A 1254 2.11 REMARK 500 O HOH A 1149 O HOH A 1267 2.11 REMARK 500 O HOH A 1031 O HOH A 1320 2.12 REMARK 500 O HOH A 612 O HOH A 728 2.12 REMARK 500 O HOH A 1249 O HOH A 1298 2.12 REMARK 500 O HOH A 1016 O HOH A 1198 2.13 REMARK 500 O ALA A 378 O HOH A 605 2.13 REMARK 500 O HOH A 816 O HOH A 1326 2.15 REMARK 500 O HOH A 801 O HOH A 1229 2.16 REMARK 500 O HOH A 905 O HOH A 1023 2.16 REMARK 500 O HOH A 776 O HOH A 1174 2.16 REMARK 500 O HOH A 1241 O HOH A 1374 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 O HOH A 1158 O HOH A 1325 6455 1.98 REMARK 500 O HOH A 783 O HOH A 1244 8554 1.99 REMARK 500 O HOH A 607 O HOH A 656 6455 2.18 REMARK 500 OE1 GLN A 254 NE2 GLN A 476 8555 2.19 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 MET A 331 CB MET A 331 CG 0.289 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 MET A 331 CB - CG - SD ANGL. DEV. = -22.9 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 ILE A 109 -55.10 -120.05 REMARK 500 ASP A 210 -168.99 -124.69 REMARK 500 LYS A 240 7.92 57.87 REMARK 500 VAL A 313 7.43 -69.59 REMARK 500 GLU A 375 -146.67 -77.60 REMARK 500 ALA A 376 -39.50 67.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1381 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A1382 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A1383 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A1384 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A1385 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A1386 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH A1387 DISTANCE = 6.67 ANGSTROMS DBREF 6K7E A 2 369 UNP P0AEX9 MALE_ECOLI 27 394 DBREF 6K7E A 387 499 UNP P53220 TIM21_YEAST 105 217 SEQADV 6K7E MET A 1 UNP P0AEX9 INITIATING METHIONINE SEQADV 6K7E VAL A 313 UNP P0AEX9 ALA 338 ENGINEERED MUTATION SEQADV 6K7E GLU A 370 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 371 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 372 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 373 UNP P0AEX9 LINKER SEQADV 6K7E LYS A 374 UNP P0AEX9 LINKER SEQADV 6K7E GLU A 375 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 376 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 377 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 378 UNP P0AEX9 LINKER SEQADV 6K7E LYS A 379 UNP P0AEX9 LINKER SEQADV 6K7E GLU A 380 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 381 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 382 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 383 UNP P0AEX9 LINKER SEQADV 6K7E LYS A 384 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 385 UNP P0AEX9 LINKER SEQADV 6K7E ALA A 386 UNP P0AEX9 LINKER SEQADV 6K7E LEU A 500 UNP P53220 EXPRESSION TAG SEQADV 6K7E GLU A 501 UNP P53220 EXPRESSION TAG SEQADV 6K7E HIS A 502 UNP P53220 EXPRESSION TAG SEQADV 6K7E HIS A 503 UNP P53220 EXPRESSION TAG SEQADV 6K7E HIS A 504 UNP P53220 EXPRESSION TAG SEQADV 6K7E HIS A 505 UNP P53220 EXPRESSION TAG SEQADV 6K7E HIS A 506 UNP P53220 EXPRESSION TAG SEQADV 6K7E HIS A 507 UNP P53220 EXPRESSION TAG SEQRES 1 A 507 MET LYS ILE GLU GLU GLY LYS LEU VAL ILE TRP ILE ASN SEQRES 2 A 507 GLY ASP LYS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS SEQRES 3 A 507 LYS PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU SEQRES 4 A 507 HIS PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA SEQRES 5 A 507 ALA THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS SEQRES 6 A 507 ASP ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA SEQRES 7 A 507 GLU ILE THR PRO ASP LYS ALA PHE GLN ASP LYS LEU TYR SEQRES 8 A 507 PRO PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU SEQRES 9 A 507 ILE ALA TYR PRO ILE ALA VAL GLU ALA LEU SER LEU ILE SEQRES 10 A 507 TYR ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP SEQRES 11 A 507 GLU GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS SEQRES 12 A 507 GLY LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR SEQRES 13 A 507 PHE THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA SEQRES 14 A 507 PHE LYS TYR GLU ASN GLY LYS TYR ASP ILE LYS ASP VAL SEQRES 15 A 507 GLY VAL ASP ASN ALA GLY ALA LYS ALA GLY LEU THR PHE SEQRES 16 A 507 LEU VAL ASP LEU ILE LYS ASN LYS HIS MET ASN ALA ASP SEQRES 17 A 507 THR ASP TYR SER ILE ALA GLU ALA ALA PHE ASN LYS GLY SEQRES 18 A 507 GLU THR ALA MET THR ILE ASN GLY PRO TRP ALA TRP SER SEQRES 19 A 507 ASN ILE ASP THR SER LYS VAL ASN TYR GLY VAL THR VAL SEQRES 20 A 507 LEU PRO THR PHE LYS GLY GLN PRO SER LYS PRO PHE VAL SEQRES 21 A 507 GLY VAL LEU SER ALA GLY ILE ASN ALA ALA SER PRO ASN SEQRES 22 A 507 LYS GLU LEU ALA LYS GLU PHE LEU GLU ASN TYR LEU LEU SEQRES 23 A 507 THR ASP GLU GLY LEU GLU ALA VAL ASN LYS ASP LYS PRO SEQRES 24 A 507 LEU GLY ALA VAL ALA LEU LYS SER TYR GLU GLU GLU LEU SEQRES 25 A 507 VAL LYS ASP PRO ARG ILE ALA ALA THR MET GLU ASN ALA SEQRES 26 A 507 GLN LYS GLY GLU ILE MET PRO ASN ILE PRO GLN MET SER SEQRES 27 A 507 ALA PHE TRP TYR ALA VAL ARG THR ALA VAL ILE ASN ALA SEQRES 28 A 507 ALA SER GLY ARG GLN THR VAL ASP GLU ALA LEU LYS ASP SEQRES 29 A 507 ALA GLN THR ARG ILE GLU ALA ALA ALA LYS GLU ALA ALA SEQRES 30 A 507 ALA LYS GLU ALA ALA ALA LYS ALA ALA ASP THR GLN LEU SEQRES 31 A 507 PHE ASN ARG ALA VAL SER MET VAL GLU LYS ASN LYS ASP SEQRES 32 A 507 ILE ARG SER LEU LEU GLN CYS ASP ASP GLY ILE THR GLY SEQRES 33 A 507 LYS GLU ARG LEU LYS ALA TYR GLY GLU LEU ILE THR ASN SEQRES 34 A 507 ASP LYS TRP THR ARG ASN ARG PRO ILE VAL SER THR LYS SEQRES 35 A 507 LYS LEU ASP LYS GLU GLY ARG THR HIS HIS TYR MET ARG SEQRES 36 A 507 PHE HIS VAL GLU SER LYS LYS LYS ILE ALA LEU VAL HIS SEQRES 37 A 507 LEU GLU ALA LYS GLU SER LYS GLN ASN TYR GLN PRO ASP SEQRES 38 A 507 PHE ILE ASN MET TYR VAL ASP VAL PRO GLY GLU LYS ARG SEQRES 39 A 507 TYR TYR LEU ILE LYS LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *787(H2 O) HELIX 1 AA1 GLY A 17 GLY A 33 1 17 HELIX 2 AA2 LYS A 43 ALA A 53 1 11 HELIX 3 AA3 ARG A 67 SER A 74 1 8 HELIX 4 AA4 ASP A 83 ASP A 88 1 6 HELIX 5 AA5 TYR A 91 ASP A 96 1 6 HELIX 6 AA6 THR A 129 GLU A 131 5 3 HELIX 7 AA7 GLU A 132 ALA A 142 1 11 HELIX 8 AA8 GLU A 154 ASP A 165 1 12 HELIX 9 AA9 ASN A 186 ASN A 202 1 17 HELIX 10 AB1 ASP A 210 LYS A 220 1 11 HELIX 11 AB2 GLY A 229 TRP A 231 5 3 HELIX 12 AB3 ALA A 232 LYS A 240 1 9 HELIX 13 AB4 ASN A 273 TYR A 284 1 12 HELIX 14 AB5 THR A 287 LYS A 298 1 12 HELIX 15 AB6 LEU A 305 VAL A 313 1 9 HELIX 16 AB7 ASP A 315 GLY A 328 1 14 HELIX 17 AB8 GLN A 336 SER A 353 1 18 HELIX 18 AB9 THR A 357 LYS A 374 1 18 HELIX 19 AC1 ALA A 376 LYS A 400 1 25 HELIX 20 AC2 ASN A 401 LEU A 408 1 8 SHEET 1 AA1 6 LYS A 35 GLU A 39 0 SHEET 2 AA1 6 LYS A 7 TRP A 11 1 N ILE A 10 O GLU A 39 SHEET 3 AA1 6 ILE A 60 ALA A 64 1 O PHE A 62 N TRP A 11 SHEET 4 AA1 6 PHE A 259 ILE A 267 -1 O GLY A 266 N ILE A 61 SHEET 5 AA1 6 TYR A 107 GLU A 112 -1 N ILE A 109 O LEU A 263 SHEET 6 AA1 6 ALA A 302 VAL A 303 -1 O ALA A 302 N VAL A 111 SHEET 1 AA2 5 LYS A 35 GLU A 39 0 SHEET 2 AA2 5 LYS A 7 TRP A 11 1 N ILE A 10 O GLU A 39 SHEET 3 AA2 5 ILE A 60 ALA A 64 1 O PHE A 62 N TRP A 11 SHEET 4 AA2 5 PHE A 259 ILE A 267 -1 O GLY A 266 N ILE A 61 SHEET 5 AA2 5 GLU A 329 ILE A 330 1 O GLU A 329 N VAL A 260 SHEET 1 AA3 2 ARG A 99 TYR A 100 0 SHEET 2 AA3 2 LYS A 103 LEU A 104 -1 O LYS A 103 N TYR A 100 SHEET 1 AA4 4 SER A 146 LEU A 148 0 SHEET 2 AA4 4 THR A 223 ASN A 228 1 O ALA A 224 N SER A 146 SHEET 3 AA4 4 SER A 115 ASN A 119 -1 N ASN A 119 O ALA A 224 SHEET 4 AA4 4 TYR A 243 THR A 246 -1 O THR A 246 N LEU A 116 SHEET 1 AA5 2 TYR A 168 GLU A 173 0 SHEET 2 AA5 2 LYS A 176 GLY A 183 -1 O LYS A 176 N GLU A 173 SHEET 1 AA6 2 THR A 250 PHE A 251 0 SHEET 2 AA6 2 GLN A 254 PRO A 255 -1 O GLN A 254 N PHE A 251 SHEET 1 AA7 3 LYS A 421 TYR A 423 0 SHEET 2 AA7 3 THR A 450 GLU A 459 -1 O HIS A 457 N TYR A 423 SHEET 3 AA7 3 SER A 440 LEU A 444 -1 N LYS A 443 O HIS A 451 SHEET 1 AA8 5 LYS A 421 TYR A 423 0 SHEET 2 AA8 5 THR A 450 GLU A 459 -1 O HIS A 457 N TYR A 423 SHEET 3 AA8 5 ILE A 464 LYS A 472 -1 O VAL A 467 N PHE A 456 SHEET 4 AA8 5 ASP A 481 ASP A 488 -1 O TYR A 486 N HIS A 468 SHEET 5 AA8 5 TYR A 495 ILE A 498 -1 O ILE A 498 N MET A 485 SHEET 1 AA9 2 ILE A 427 THR A 428 0 SHEET 2 AA9 2 LYS A 431 TRP A 432 -1 O LYS A 431 N THR A 428 CRYST1 156.807 156.807 67.386 90.00 90.00 120.00 H 3 9 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 0.006377 0.003682 0.000000 0.00000 SCALE2 0.000000 0.007364 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014840 0.00000