PDB Short entry for 4IKV HEADER TRANSPORT PROTEIN 28-DEC-12 4IKV TITLE CRYSTAL STRUCTURE OF PEPTIDE TRANSPORTER POT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DI-TRIPEPTIDE ABC TRANSPORTER (PERMEASE); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS; SOURCE 3 ORGANISM_TAXID: 1462; SOURCE 4 STRAIN: BD53; SOURCE 5 GENE: GK2020; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41(DE3)DELTA-ACRB; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCGFP-BC KEYWDS MAJOR FACILITATOR SUPERFAMILY, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.DOKI,H.E.KATO,R.ISHITANI,O.NUREKI REVDAT 3 03-APR-24 4IKV 1 REMARK REVDAT 2 24-AUG-22 4IKV 1 JRNL REMARK REVDAT 1 10-JUL-13 4IKV 0 JRNL AUTH S.DOKI,H.E.KATO,N.SOLCAN,M.IWAKI,M.KOYAMA,M.HATTORI,N.IWASE, JRNL AUTH 2 T.TSUKAZAKI,Y.SUGITA,H.KANDORI,S.NEWSTEAD,R.ISHITANI, JRNL AUTH 3 O.NUREKI JRNL TITL STRUCTURAL BASIS FOR DYNAMIC MECHANISM OF PROTON-COUPLED JRNL TITL 2 SYMPORT BY THE PEPTIDE TRANSPORTER POT. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 11343 2013 JRNL REFN ESSN 1091-6490 JRNL PMID 23798427 JRNL DOI 10.1073/PNAS.1301079110 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.560 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.4 REMARK 3 NUMBER OF REFLECTIONS : 35267 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1764 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 32.3517 - 4.4640 0.97 2886 152 0.2104 0.2186 REMARK 3 2 4.4640 - 3.5446 0.98 2881 152 0.1825 0.2191 REMARK 3 3 3.5446 - 3.0970 0.97 2845 150 0.1762 0.2078 REMARK 3 4 3.0970 - 2.8140 0.96 2790 146 0.1815 0.2448 REMARK 3 5 2.8140 - 2.6124 0.94 2729 144 0.1692 0.2214 REMARK 3 6 2.6124 - 2.4584 0.93 2695 142 0.1538 0.1869 REMARK 3 7 2.4584 - 2.3353 0.90 2629 139 0.1517 0.1829 REMARK 3 8 2.3353 - 2.2337 0.89 2600 136 0.1440 0.2038 REMARK 3 9 2.2337 - 2.1477 0.85 2464 130 0.1635 0.1993 REMARK 3 10 2.1477 - 2.0736 0.82 2374 125 0.1689 0.1851 REMARK 3 11 2.0736 - 2.0088 0.80 2334 123 0.1831 0.2449 REMARK 3 12 2.0088 - 1.9514 0.75 2162 113 0.1962 0.2498 REMARK 3 13 1.9514 - 1.9000 0.73 2114 112 0.2261 0.2647 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 : 0.86 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 80.06 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.10010 REMARK 3 B22 (A**2) : -4.05240 REMARK 3 B33 (A**2) : -6.04780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.25190 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 3943 REMARK 3 ANGLE : 1.053 5340 REMARK 3 CHIRALITY : 0.070 609 REMARK 3 PLANARITY : 0.005 647 REMARK 3 DIHEDRAL : 14.726 1388 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 2:51) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2307 27.0954 10.9274 REMARK 3 T TENSOR REMARK 3 T11: 0.2240 T22: 0.2277 REMARK 3 T33: 0.2122 T12: 0.0301 REMARK 3 T13: 0.0041 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 0.3663 L22: 0.2151 REMARK 3 L33: 0.5653 L12: -0.0507 REMARK 3 L13: -0.0162 L23: -0.3460 REMARK 3 S TENSOR REMARK 3 S11: -0.0363 S12: -0.0403 S13: 0.0088 REMARK 3 S21: 0.0969 S22: 0.0280 S23: 0.0323 REMARK 3 S31: -0.1544 S32: -0.1217 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 52:113) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6762 25.8109 -0.2477 REMARK 3 T TENSOR REMARK 3 T11: 0.2075 T22: 0.1851 REMARK 3 T33: 0.2139 T12: 0.0081 REMARK 3 T13: -0.0123 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.6680 L22: 1.0771 REMARK 3 L33: 0.6467 L12: 0.0562 REMARK 3 L13: -0.5999 L23: -0.3171 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: -0.0254 S13: 0.0270 REMARK 3 S21: -0.0109 S22: -0.0238 S23: -0.1016 REMARK 3 S31: -0.0059 S32: 0.0121 S33: -0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 114:223) REMARK 3 ORIGIN FOR THE GROUP (A): 14.1156 28.0166 8.0200 REMARK 3 T TENSOR REMARK 3 T11: 0.1397 T22: 0.0953 REMARK 3 T33: 0.1433 T12: 0.0287 REMARK 3 T13: -0.0001 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 1.3815 L22: 1.3488 REMARK 3 L33: 0.8303 L12: 0.1524 REMARK 3 L13: -0.7091 L23: -0.1975 REMARK 3 S TENSOR REMARK 3 S11: 0.0190 S12: -0.0472 S13: 0.0046 REMARK 3 S21: 0.1361 S22: 0.0194 S23: -0.0114 REMARK 3 S31: -0.1158 S32: 0.0150 S33: -0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 224:255) REMARK 3 ORIGIN FOR THE GROUP (A): 43.9645 27.6708 2.6629 REMARK 3 T TENSOR REMARK 3 T11: 0.5158 T22: 0.3693 REMARK 3 T33: 0.5454 T12: 0.1586 REMARK 3 T13: -0.1077 T23: -0.1023 REMARK 3 L TENSOR REMARK 3 L11: 0.6830 L22: 0.1063 REMARK 3 L33: -0.0130 L12: 0.3688 REMARK 3 L13: -0.0177 L23: 0.0302 REMARK 3 S TENSOR REMARK 3 S11: -0.1566 S12: -0.0278 S13: 0.6820 REMARK 3 S21: 0.3272 S22: 0.3328 S23: -1.0438 REMARK 3 S31: -0.0871 S32: 0.6616 S33: -0.1199 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 256:285) REMARK 3 ORIGIN FOR THE GROUP (A): 37.2659 10.5224 8.9909 REMARK 3 T TENSOR REMARK 3 T11: 0.2059 T22: 0.3598 REMARK 3 T33: 0.3244 T12: -0.0519 REMARK 3 T13: -0.0395 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.0803 L22: 0.6172 REMARK 3 L33: 0.1300 L12: -0.2406 REMARK 3 L13: -0.1202 L23: 0.2837 REMARK 3 S TENSOR REMARK 3 S11: 0.1589 S12: -0.0036 S13: -0.0529 REMARK 3 S21: 0.2563 S22: -0.0946 S23: -0.1363 REMARK 3 S31: -0.2757 S32: 0.6677 S33: 0.0021 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 286:334) REMARK 3 ORIGIN FOR THE GROUP (A): 19.0377 6.3775 -0.1870 REMARK 3 T TENSOR REMARK 3 T11: 0.1192 T22: 0.1555 REMARK 3 T33: 0.1870 T12: -0.0010 REMARK 3 T13: 0.0225 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.5917 L22: 1.7201 REMARK 3 L33: 0.4660 L12: 0.1847 REMARK 3 L13: -0.5817 L23: 0.2359 REMARK 3 S TENSOR REMARK 3 S11: -0.0472 S12: 0.0614 S13: 0.0734 REMARK 3 S21: -0.1248 S22: -0.0316 S23: 0.0416 REMARK 3 S31: 0.0226 S32: -0.0685 S33: -0.0001 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 335:427) REMARK 3 ORIGIN FOR THE GROUP (A): 10.6878 2.3076 3.5070 REMARK 3 T TENSOR REMARK 3 T11: 0.1684 T22: 0.2040 REMARK 3 T33: 0.2172 T12: -0.0114 REMARK 3 T13: 0.0103 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.7633 L22: 1.8023 REMARK 3 L33: 0.4456 L12: -0.2652 REMARK 3 L13: 0.1006 L23: -0.6916 REMARK 3 S TENSOR REMARK 3 S11: 0.0235 S12: -0.0463 S13: -0.1280 REMARK 3 S21: -0.0137 S22: 0.1161 S23: 0.1616 REMARK 3 S31: 0.1103 S32: -0.1157 S33: 0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 428:459) REMARK 3 ORIGIN FOR THE GROUP (A): 27.4914 10.0799 5.6653 REMARK 3 T TENSOR REMARK 3 T11: 0.1851 T22: 0.2161 REMARK 3 T33: 0.2344 T12: 0.0111 REMARK 3 T13: -0.0193 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: -0.0560 L22: 0.7644 REMARK 3 L33: 0.4629 L12: -0.1393 REMARK 3 L13: 0.2539 L23: -0.5998 REMARK 3 S TENSOR REMARK 3 S11: 0.0123 S12: -0.0363 S13: 0.1396 REMARK 3 S21: 0.1648 S22: -0.0328 S23: -0.1532 REMARK 3 S31: -0.0591 S32: 0.0162 S33: 0.0250 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 460:493) REMARK 3 ORIGIN FOR THE GROUP (A): 23.0255 -4.7112 3.7875 REMARK 3 T TENSOR REMARK 3 T11: 0.3103 T22: 0.1956 REMARK 3 T33: 0.1964 T12: 0.0211 REMARK 3 T13: -0.0366 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.4426 L22: 0.8389 REMARK 3 L33: 0.0916 L12: 0.0677 REMARK 3 L13: -0.1908 L23: 0.0154 REMARK 3 S TENSOR REMARK 3 S11: 0.0007 S12: -0.1249 S13: -0.0918 REMARK 3 S21: 0.2139 S22: 0.0350 S23: -0.0143 REMARK 3 S31: -0.1352 S32: -0.0848 S33: -0.0001 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 4IKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076879. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35439 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 88.2 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.20100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: SEM-SUBSTITUTED PROTEIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 400, 100 MM ADA-NAOH, 160 MM REMARK 280 LI2SO4, 4 MM SRCL2, PH 6.5, LIPIDIC CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 47.45850 REMARK 290 SMTRY3 2 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 MET A 1 REMARK 465 GLY A 494 REMARK 465 ILE A 495 REMARK 465 ARG A 496 REMARK 465 LEU A 497 REMARK 465 GLU A 498 REMARK 465 SER A 499 REMARK 465 SER A 500 REMARK 465 GLY A 501 REMARK 465 GLU A 502 REMARK 465 ASN A 503 REMARK 465 LEU A 504 REMARK 465 TYR A 505 REMARK 465 PHE A 506 REMARK 465 GLN A 507 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 96 CD NE CZ NH1 NH2 REMARK 470 LYS A 208 CG CD CE NZ REMARK 470 LYS A 227 CE NZ REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 LYS A 229 CG CD CE NZ REMARK 470 VAL A 239 CG1 CG2 REMARK 470 GLU A 461 CG CD OE1 OE2 REMARK 470 LYS A 493 CG CD CE NZ 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 O25 OLB A 612 O HOH A 812 2646 2.03 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 LEU A 135 CA - CB - CG ANGL. DEV. = 17.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 91 -53.88 -132.35 REMARK 500 VAL A 175 -61.75 -94.35 REMARK 500 TYR A 183 -59.55 -121.77 REMARK 500 ASN A 184 130.86 -170.11 REMARK 500 THR A 314 -87.56 -120.24 REMARK 500 ALA A 329 -143.80 58.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 OLA A 605 REMARK 610 OLA A 606 REMARK 610 OLA A 607 REMARK 610 OLA A 608 REMARK 610 OLA A 609 REMARK 610 OLA A 610 REMARK 610 OLA A 611 REMARK 610 OLB A 612 REMARK 610 PG4 A 613 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLB A 612 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 613 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IKW RELATED DB: PDB REMARK 900 RELATED ID: 4IKX RELATED DB: PDB REMARK 900 RELATED ID: 4IKY RELATED DB: PDB REMARK 900 RELATED ID: 4IKZ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM STRAIN BD53 OF REMARK 999 GEOBACILLUS SPECIES WHOSE SEQUENCE IS NOT AVAILABLE IN THE UNIPROT REMARK 999 DATABASE. THE SEQUENCE CONSTRUCT IS THE SAME AS Q5KYD1_GEOKA. C- REMARK 999 TERMINAL RESIDUES LESSGENLYFQ ARE EXPRESSION TAGS. DBREF 4IKV A 1 507 PDB 4IKV 4IKV 1 507 SEQRES 1 A 507 MET ALA SER ILE ASP LYS GLN GLN ILE ALA ALA SER VAL SEQRES 2 A 507 PRO GLN ARG GLY PHE PHE GLY HIS PRO LYS GLY LEU PHE SEQRES 3 A 507 THR LEU PHE PHE THR GLU PHE TRP GLU ARG PHE SER TYR SEQRES 4 A 507 TYR GLY MET ARG ALA ILE LEU VAL TYR TYR MET TYR TYR SEQRES 5 A 507 GLU VAL SER LYS GLY GLY LEU GLY LEU ASP GLU HIS LEU SEQRES 6 A 507 ALA LEU ALA ILE MET SER ILE TYR GLY ALA LEU VAL TYR SEQRES 7 A 507 MET SER GLY ILE ILE GLY GLY TRP LEU ALA ASP ARG VAL SEQRES 8 A 507 PHE GLY THR SER ARG ALA VAL PHE TYR GLY GLY LEU LEU SEQRES 9 A 507 ILE MET ALA GLY HIS ILE ALA LEU ALA ILE PRO GLY GLY SEQRES 10 A 507 VAL ALA ALA LEU PHE VAL SER MET ALA LEU ILE VAL LEU SEQRES 11 A 507 GLY THR GLY LEU LEU LYS PRO ASN VAL SER SER ILE VAL SEQRES 12 A 507 GLY ASP MET TYR LYS PRO GLY ASP ASP ARG ARG ASP ALA SEQRES 13 A 507 GLY PHE SER ILE PHE TYR MET GLY ILE ASN LEU GLY ALA SEQRES 14 A 507 PHE LEU ALA PRO LEU VAL VAL GLY THR ALA GLY MET LYS SEQRES 15 A 507 TYR ASN PHE HIS LEU GLY PHE GLY LEU ALA ALA VAL GLY SEQRES 16 A 507 MET PHE LEU GLY LEU VAL VAL PHE VAL ALA THR ARG LYS SEQRES 17 A 507 LYS ASN LEU GLY LEU ALA GLY THR TYR VAL PRO ASN PRO SEQRES 18 A 507 LEU THR PRO ALA GLU LYS LYS LYS ALA ALA ALA ILE MET SEQRES 19 A 507 ALA VAL GLY ALA VAL VAL ILE ALA VAL LEU LEU ALA ILE SEQRES 20 A 507 LEU ILE PRO ASN GLY TRP PHE THR VAL GLU THR PHE ILE SEQRES 21 A 507 SER LEU VAL GLY ILE LEU GLY ILE ILE ILE PRO ILE ILE SEQRES 22 A 507 TYR PHE VAL VAL MET TYR ARG SER PRO LYS THR THR ALA SEQRES 23 A 507 GLU GLU ARG SER ARG VAL ILE ALA TYR ILE PRO LEU PHE SEQRES 24 A 507 VAL ALA SER ALA MET PHE TRP ALA ILE GLN GLU GLN GLY SEQRES 25 A 507 SER THR ILE LEU ALA ASN TYR ALA ASP LYS ARG THR GLN SEQRES 26 A 507 LEU ASP VAL ALA GLY ILE HIS LEU SER PRO ALA TRP PHE SEQRES 27 A 507 GLN SER LEU ASN PRO LEU PHE ILE ILE ILE LEU ALA PRO SEQRES 28 A 507 VAL PHE ALA TRP MET TRP VAL LYS LEU GLY LYS ARG GLN SEQRES 29 A 507 PRO THR ILE PRO GLN LYS PHE ALA LEU GLY LEU LEU PHE SEQRES 30 A 507 ALA GLY LEU SER PHE ILE VAL ILE LEU VAL PRO GLY HIS SEQRES 31 A 507 LEU SER GLY GLY GLY LEU VAL HIS PRO ILE TRP LEU VAL SEQRES 32 A 507 LEU SER TYR PHE ILE VAL VAL LEU GLY GLU LEU CYS LEU SEQRES 33 A 507 SER PRO VAL GLY LEU SER ALA THR THR LYS LEU ALA PRO SEQRES 34 A 507 ALA ALA PHE SER ALA GLN THR MET SER LEU TRP PHE LEU SEQRES 35 A 507 SER ASN ALA ALA ALA GLN ALA ILE ASN ALA GLN LEU VAL SEQRES 36 A 507 ARG PHE TYR THR PRO GLU ASN GLU THR ALA TYR PHE GLY SEQRES 37 A 507 THR ILE GLY GLY ALA ALA LEU VAL LEU GLY LEU ILE LEU SEQRES 38 A 507 LEU ALA ILE ALA PRO ARG ILE GLY ARG LEU MET LYS GLY SEQRES 39 A 507 ILE ARG LEU GLU SER SER GLY GLU ASN LEU TYR PHE GLN HET SO4 A 601 5 HET SO4 A 602 5 HET SO4 A 603 5 HET SO4 A 604 5 HET OLA A 605 8 HET OLA A 606 16 HET OLA A 607 11 HET OLA A 608 15 HET OLA A 609 10 HET OLA A 610 10 HET OLA A 611 8 HET OLB A 612 14 HET PG4 A 613 10 HETNAM SO4 SULFATE ION HETNAM OLA OLEIC ACID HETNAM OLB (2S)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 OLA 7(C18 H34 O2) FORMUL 13 OLB C21 H40 O4 FORMUL 14 PG4 C8 H18 O5 FORMUL 15 HOH *141(H2 O) HELIX 1 1 ASP A 5 ALA A 11 1 7 HELIX 2 2 LYS A 23 TYR A 52 1 30 HELIX 3 3 GLU A 53 GLY A 57 5 5 HELIX 4 4 ASP A 62 VAL A 91 1 30 HELIX 5 5 GLY A 93 ILE A 114 1 22 HELIX 6 6 GLY A 117 LYS A 136 1 20 HELIX 7 7 ASN A 138 MET A 146 1 9 HELIX 8 8 ARG A 153 TYR A 183 1 31 HELIX 9 9 ASN A 184 GLY A 212 1 29 HELIX 10 10 THR A 223 ILE A 249 1 27 HELIX 11 11 THR A 255 SER A 281 1 27 HELIX 12 12 THR A 285 GLN A 311 1 27 HELIX 13 13 THR A 314 ARG A 323 1 10 HELIX 14 14 SER A 334 GLN A 339 5 6 HELIX 15 15 SER A 340 GLY A 361 1 22 HELIX 16 16 LYS A 362 GLN A 364 5 3 HELIX 17 17 THR A 366 GLY A 393 1 28 HELIX 18 18 PRO A 399 SER A 417 1 19 HELIX 19 19 VAL A 419 ALA A 428 1 10 HELIX 20 20 PRO A 429 ALA A 434 5 6 HELIX 21 21 GLN A 435 VAL A 455 1 21 HELIX 22 22 ARG A 456 TYR A 458 5 3 HELIX 23 23 THR A 459 GLU A 461 5 3 HELIX 24 24 ASN A 462 MET A 492 1 31 SHEET 1 A 2 GLY A 17 PHE A 18 0 SHEET 2 A 2 HIS A 21 PRO A 22 -1 O HIS A 21 N PHE A 18 SITE 1 AC1 5 ALA A 2 THR A 216 TYR A 217 VAL A 218 SITE 2 AC1 5 HOH A 806 SITE 1 AC2 4 ARG A 16 GLY A 17 PHE A 19 GLY A 20 SITE 1 AC3 2 LYS A 148 HOH A 758 SITE 1 AC4 4 PRO A 14 GLN A 15 ARG A 16 HOH A 815 SITE 1 AC5 1 PRO A 297 SITE 1 AC6 3 PRO A 115 VAL A 194 OLA A 607 SITE 1 AC7 3 ASN A 184 HIS A 186 OLA A 606 SITE 1 AC8 2 ALA A 465 GLY A 468 SITE 1 AC9 1 OLA A 610 SITE 1 BC1 2 LEU A 373 OLA A 609 SITE 1 BC2 2 GLN A 369 LEU A 482 SITE 1 BC3 6 TRP A 357 GLN A 364 PRO A 365 THR A 366 SITE 2 BC3 6 ILE A 367 LYS A 370 CRYST1 50.761 94.917 57.253 90.00 111.10 90.00 P 1 21 1 2 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 0.019700 0.000000 0.007603 0.00000 SCALE2 0.000000 0.010536 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018722 0.00000