HEADER TRANSFERASE 20-DEC-14 4XDU TITLE CRYSTAL STRUCTURE OF TREPONEMA PALLIDUM TP0796 FLAVIN TRAFFICKING TITLE 2 PROTEIN,A BIFUNCTIONAL FMN TRANSFERASE/FAD PYROPHOSPHATASE, N55Y TITLE 3 MUTANT, ADP BOUND FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAD:PROTEIN FMN TRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FLAVIN TRANSFERASE; COMPND 5 EC: 2.7.1.180; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TREPONEMA PALLIDUM (STRAIN NICHOLS); SOURCE 3 ORGANISM_TAXID: 243276; SOURCE 4 STRAIN: NICHOLS; SOURCE 5 GENE: APBE, TP_0796; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS FMN TRANSFERASE, FAD PYROPHOSPHATASE, HYDROLASE, BIMETAL CENTER, KEYWDS 2 FLAVIN TURNOVER, TREPONEMA PALLIDUM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.R.TOMCHICK,C.A.BRAUTIGAM,R.K.DEKA,M.V.NORGARD REVDAT 2 28-FEB-24 4XDU 1 REMARK LINK REVDAT 1 14-OCT-15 4XDU 0 JRNL AUTH R.K.DEKA,C.A.BRAUTIGAM,W.Z.LIU,D.R.TOMCHICK,M.V.NORGARD JRNL TITL EVIDENCE FOR POSTTRANSLATIONAL PROTEIN FLAVINYLATION IN THE JRNL TITL 2 SYPHILIS SPIROCHETE TREPONEMA PALLIDUM: STRUCTURAL AND JRNL TITL 3 BIOCHEMICAL INSIGHTS FROM THE CATALYTIC CORE OF A JRNL TITL 4 PERIPLASMIC FLAVIN-TRAFFICKING PROTEIN. JRNL REF MBIO V. 6 00519 2015 JRNL REFN ESSN 2150-7511 JRNL PMID 25944861 JRNL DOI 10.1128/MBIO.00519-15 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 66598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3361 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 24.5386 - 3.8891 0.99 2729 141 0.1636 0.1849 REMARK 3 2 3.8891 - 3.0889 1.00 2699 136 0.1682 0.1691 REMARK 3 3 3.0889 - 2.6990 1.00 2703 124 0.1653 0.2006 REMARK 3 4 2.6990 - 2.4524 1.00 2616 151 0.1628 0.1708 REMARK 3 5 2.4524 - 2.2768 1.00 2677 143 0.1510 0.1535 REMARK 3 6 2.2768 - 2.1426 1.00 2632 143 0.1471 0.1518 REMARK 3 7 2.1426 - 2.0354 1.00 2636 140 0.1552 0.1883 REMARK 3 8 2.0354 - 1.9468 1.00 2652 127 0.1524 0.1935 REMARK 3 9 1.9468 - 1.8719 1.00 2634 147 0.1593 0.1826 REMARK 3 10 1.8719 - 1.8073 1.00 2639 142 0.1617 0.1899 REMARK 3 11 1.8073 - 1.7508 1.00 2648 125 0.1643 0.2091 REMARK 3 12 1.7508 - 1.7008 1.00 2617 148 0.1671 0.1871 REMARK 3 13 1.7008 - 1.6560 1.00 2629 143 0.1658 0.2181 REMARK 3 14 1.6560 - 1.6156 1.00 2639 152 0.1717 0.2148 REMARK 3 15 1.6156 - 1.5789 1.00 2652 122 0.1736 0.2226 REMARK 3 16 1.5789 - 1.5453 1.00 2616 159 0.1734 0.1996 REMARK 3 17 1.5453 - 1.5144 1.00 2629 144 0.1717 0.1829 REMARK 3 18 1.5144 - 1.4858 1.00 2621 151 0.1827 0.1968 REMARK 3 19 1.4858 - 1.4593 1.00 2595 147 0.1892 0.2222 REMARK 3 20 1.4593 - 1.4346 1.00 2633 158 0.2044 0.2097 REMARK 3 21 1.4346 - 1.4114 1.00 2629 130 0.2136 0.2271 REMARK 3 22 1.4114 - 1.3897 1.00 2619 137 0.2336 0.2996 REMARK 3 23 1.3897 - 1.3693 0.98 2553 139 0.2484 0.2788 REMARK 3 24 1.3693 - 1.3500 0.95 2540 112 0.2618 0.2541 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.64 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 : 0.016 2664 REMARK 3 ANGLE : 1.243 3586 REMARK 3 CHIRALITY : 0.074 416 REMARK 3 PLANARITY : 0.005 462 REMARK 3 DIHEDRAL : 13.561 953 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.7697 21.5985 -0.1304 REMARK 3 T TENSOR REMARK 3 T11: 0.0293 T22: 0.1088 REMARK 3 T33: 0.0828 T12: 0.0053 REMARK 3 T13: 0.0161 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 2.3108 L22: 2.9340 REMARK 3 L33: 4.7559 L12: 0.5391 REMARK 3 L13: -0.8870 L23: -0.7928 REMARK 3 S TENSOR REMARK 3 S11: 0.0519 S12: 0.0318 S13: 0.0295 REMARK 3 S21: -0.0604 S22: -0.0663 S23: -0.0058 REMARK 3 S31: 0.1207 S32: 0.2545 S33: 0.0681 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.4716 24.8181 16.7005 REMARK 3 T TENSOR REMARK 3 T11: 0.2197 T22: 0.1292 REMARK 3 T33: 0.1393 T12: 0.0088 REMARK 3 T13: 0.0500 T23: -0.0133 REMARK 3 L TENSOR REMARK 3 L11: 1.5914 L22: 0.4372 REMARK 3 L33: 1.9195 L12: 0.3976 REMARK 3 L13: -1.4025 L23: -0.8123 REMARK 3 S TENSOR REMARK 3 S11: 0.2194 S12: -0.1824 S13: 0.1110 REMARK 3 S21: 0.3059 S22: -0.0689 S23: 0.0602 REMARK 3 S31: -0.3679 S32: 0.0945 S33: -0.1161 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.6506 7.7939 30.3760 REMARK 3 T TENSOR REMARK 3 T11: 0.3106 T22: 0.2468 REMARK 3 T33: 0.1646 T12: 0.0269 REMARK 3 T13: 0.0253 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 3.2731 L22: 3.1388 REMARK 3 L33: 4.5794 L12: -0.3168 REMARK 3 L13: 0.1822 L23: 0.5563 REMARK 3 S TENSOR REMARK 3 S11: 0.0025 S12: -0.4489 S13: -0.2153 REMARK 3 S21: 0.7901 S22: 0.1712 S23: -0.2706 REMARK 3 S31: 0.4948 S32: 0.4863 S33: -0.0680 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.7098 19.9238 8.5214 REMARK 3 T TENSOR REMARK 3 T11: 0.0908 T22: 0.0760 REMARK 3 T33: 0.0882 T12: -0.0030 REMARK 3 T13: 0.0243 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.5264 L22: 0.9128 REMARK 3 L33: 0.2321 L12: -0.2844 REMARK 3 L13: 0.2535 L23: -0.3463 REMARK 3 S TENSOR REMARK 3 S11: -0.0519 S12: -0.0335 S13: -0.0069 REMARK 3 S21: 0.0937 S22: 0.0451 S23: 0.0656 REMARK 3 S31: -0.0091 S32: -0.0444 S33: 0.0091 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 217 THROUGH 279 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.7820 1.8510 13.8032 REMARK 3 T TENSOR REMARK 3 T11: 0.1071 T22: 0.0982 REMARK 3 T33: 0.1047 T12: -0.0010 REMARK 3 T13: -0.0055 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.5382 L22: 1.8718 REMARK 3 L33: 3.1021 L12: 0.0080 REMARK 3 L13: -0.1995 L23: -1.1254 REMARK 3 S TENSOR REMARK 3 S11: -0.0128 S12: -0.0888 S13: -0.0460 REMARK 3 S21: 0.1606 S22: -0.0240 S23: -0.1034 REMARK 3 S31: 0.1239 S32: 0.2293 S33: 0.0469 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 280 THROUGH 340 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.6979 -0.5073 4.4554 REMARK 3 T TENSOR REMARK 3 T11: 0.0842 T22: 0.0799 REMARK 3 T33: 0.0975 T12: -0.0117 REMARK 3 T13: -0.0017 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.2423 L22: 2.3212 REMARK 3 L33: 1.0267 L12: -0.6319 REMARK 3 L13: -0.4608 L23: 0.3088 REMARK 3 S TENSOR REMARK 3 S11: 0.0318 S12: 0.1135 S13: -0.1214 REMARK 3 S21: -0.0488 S22: -0.0720 S23: 0.2275 REMARK 3 S31: 0.0656 S32: -0.0563 S33: 0.0384 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 4XDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205499. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-12 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72901 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.50900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 0.7 M SODIUM ACETATE, 0.1 M REMARK 280 NACL, 20% (V/V) ETHYLENE GLYCOL;, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING 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 58.41500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.40700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.41500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.40700 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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER. THERE IS 1 BIOLOGICAL REMARK 300 UNIT IN THE ASYMMETRIC UNIT. 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 646 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 713 LIES ON A SPECIAL POSITION. 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 CYS A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 REMARK 465 ARG A 4 REMARK 465 ASP A 201 REMARK 465 VAL A 202 REMARK 465 ARG A 203 REMARK 465 SER A 204 REMARK 465 ALA A 205 REMARK 465 ALA A 206 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 HE ARG A 29 OE1 GLU A 33 1.52 REMARK 500 O HOH A 796 O HOH A 802 2.19 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 SER A 70 -149.72 -121.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 162 O REMARK 620 2 ASP A 284 O 92.8 REMARK 620 3 ASP A 284 OD1 83.5 91.3 REMARK 620 4 THR A 288 OG1 111.3 94.8 163.5 REMARK 620 5 ADP A 505 O1A 103.8 160.1 79.9 89.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 239 O REMARK 620 2 GLU A 244 OE1 103.2 REMARK 620 3 ADP A 505 O3B 111.3 81.5 REMARK 620 4 HOH A 787 O 151.6 104.4 79.6 REMARK 620 5 HOH A 789 O 98.2 154.6 103.5 53.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 267 O REMARK 620 2 EDO A 508 O1 78.6 REMARK 620 3 HOH A 735 O 95.7 76.8 REMARK 620 4 HOH A 816 O 172.2 96.7 89.2 REMARK 620 5 HOH A 823 O 92.7 105.0 171.6 82.5 REMARK 620 6 HOH A 851 O 92.9 155.6 81.5 93.9 98.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 284 OD1 REMARK 620 2 ADP A 505 O1B 173.5 REMARK 620 3 ADP A 505 O1A 89.6 89.2 REMARK 620 4 HOH A 717 O 84.2 89.5 93.0 REMARK 620 5 HOH A 718 O 91.4 94.8 85.4 175.3 REMARK 620 6 HOH A 850 O 90.6 91.4 174.3 92.7 88.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 510 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IFU RELATED DB: PDB REMARK 900 4IFU CONTAINS THE WILD TYPE PROTEIN, APO FORM. DBREF 4XDU A 1 340 UNP O83774 APBE_TREPA 23 362 SEQADV 4XDU TYR A 55 UNP O83774 ASN 77 ENGINEERED MUTATION SEQADV 4XDU VAL A 104 UNP O83774 UNK 126 CONFLICT SEQRES 1 A 340 CYS GLY GLY ARG ALA ARG VAL ARG GLU TYR SER ARG ALA SEQRES 2 A 340 GLU LEU VAL ILE GLY THR LEU CYS ARG VAL ARG VAL TYR SEQRES 3 A 340 SER LYS ARG PRO ALA ALA GLU VAL HIS ALA ALA LEU GLU SEQRES 4 A 340 GLU VAL PHE THR LEU LEU GLN GLN GLN GLU MET VAL LEU SEQRES 5 A 340 SER ALA TYR ARG ASP ASP SER ALA LEU ALA ALA LEU ASN SEQRES 6 A 340 ALA GLN ALA GLY SER ALA PRO VAL VAL VAL ASP ARG SER SEQRES 7 A 340 LEU TYR ALA LEU LEU GLU ARG ALA LEU PHE PHE ALA GLU SEQRES 8 A 340 LYS SER GLY GLY ALA PHE ASN PRO ALA LEU GLY ALA VAL SEQRES 9 A 340 VAL LYS LEU TRP ASN ILE GLY PHE ASP ARG ALA ALA VAL SEQRES 10 A 340 PRO ASP PRO ASP ALA LEU LYS GLU ALA LEU THR ARG CYS SEQRES 11 A 340 ASP PHE ARG GLN VAL HIS LEU ARG ALA GLY VAL SER VAL SEQRES 12 A 340 GLY ALA PRO HIS THR VAL GLN LEU ALA GLN ALA GLY MET SEQRES 13 A 340 GLN LEU ASP LEU GLY ALA ILE ALA LYS GLY PHE LEU ALA SEQRES 14 A 340 ASP LYS ILE VAL GLN LEU LEU THR ALA HIS ALA LEU ASP SEQRES 15 A 340 SER ALA LEU VAL ASP LEU GLY GLY ASN ILE PHE ALA LEU SEQRES 16 A 340 GLY LEU LYS TYR GLY ASP VAL ARG SER ALA ALA ALA GLN SEQRES 17 A 340 ARG LEU GLU TRP ASN VAL GLY ILE ARG ASP PRO HIS GLY SEQRES 18 A 340 THR GLY GLN LYS PRO ALA LEU VAL VAL SER VAL ARG ASP SEQRES 19 A 340 CYS SER VAL VAL THR SER GLY ALA TYR GLU ARG PHE PHE SEQRES 20 A 340 GLU ARG ASP GLY VAL ARG TYR HIS HIS ILE ILE ASP PRO SEQRES 21 A 340 VAL THR GLY PHE PRO ALA HIS THR ASP VAL ASP SER VAL SEQRES 22 A 340 SER ILE PHE ALA PRO ARG SER THR ASP ALA ASP ALA LEU SEQRES 23 A 340 ALA THR ALA CYS PHE VAL LEU GLY TYR GLU LYS SER CYS SEQRES 24 A 340 ALA LEU LEU ARG GLU PHE PRO GLY VAL ASP ALA LEU PHE SEQRES 25 A 340 ILE PHE PRO ASP LYS ARG VAL ARG ALA SER ALA GLY ILE SEQRES 26 A 340 VAL ASP ARG VAL ARG VAL LEU ASP ALA ARG PHE VAL LEU SEQRES 27 A 340 GLU ARG HET MG A 501 1 HET MG A 502 1 HET NA A 503 1 HET NA A 504 1 HET ADP A 505 39 HET EDO A 506 10 HET EDO A 507 10 HET EDO A 508 10 HET ACT A 509 7 HET ACT A 510 7 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG 2(MG 2+) FORMUL 4 NA 2(NA 1+) FORMUL 6 ADP C10 H15 N5 O10 P2 FORMUL 7 EDO 3(C2 H6 O2) FORMUL 10 ACT 2(C2 H3 O2 1-) FORMUL 12 HOH *255(H2 O) HELIX 1 AA1 PRO A 30 SER A 53 1 24 HELIX 2 AA2 SER A 59 GLN A 67 1 9 HELIX 3 AA3 ASP A 76 SER A 93 1 18 HELIX 4 AA4 LEU A 101 ALA A 115 1 15 HELIX 5 AA5 ASP A 119 THR A 128 1 10 HELIX 6 AA6 ARG A 129 CYS A 130 5 2 HELIX 7 AA7 ASP A 131 ARG A 133 5 3 HELIX 8 AA8 ILE A 163 HIS A 179 1 17 HELIX 9 AA9 ARG A 279 GLY A 294 1 16 HELIX 10 AB1 GLY A 294 ARG A 303 1 10 HELIX 11 AB2 ILE A 325 ASP A 327 5 3 SHEET 1 AA1 9 ARG A 8 VAL A 16 0 SHEET 2 AA1 9 THR A 19 SER A 27 -1 O VAL A 25 N TYR A 10 SHEET 3 AA1 9 ALA A 184 LEU A 188 -1 O ASP A 187 N ARG A 22 SHEET 4 AA1 9 ASN A 191 LEU A 195 -1 O PHE A 193 N VAL A 186 SHEET 5 AA1 9 CYS A 235 GLY A 241 -1 O CYS A 235 N ALA A 194 SHEET 6 AA1 9 SER A 272 ALA A 277 -1 O ALA A 277 N SER A 236 SHEET 7 AA1 9 ASP A 309 ILE A 313 -1 O LEU A 311 N SER A 274 SHEET 8 AA1 9 ARG A 318 ALA A 321 -1 O ARG A 320 N PHE A 312 SHEET 9 AA1 9 VAL A 337 LEU A 338 1 O VAL A 337 N VAL A 319 SHEET 1 AA2 3 VAL A 73 VAL A 75 0 SHEET 2 AA2 3 HIS A 147 LEU A 151 -1 O VAL A 149 N VAL A 73 SHEET 3 AA2 3 VAL A 135 ALA A 139 -1 N ARG A 138 O THR A 148 SHEET 1 AA3 2 LYS A 198 TYR A 199 0 SHEET 2 AA3 2 ARG A 209 LEU A 210 -1 O LEU A 210 N LYS A 198 SHEET 1 AA4 3 TRP A 212 ARG A 217 0 SHEET 2 AA4 3 PRO A 226 VAL A 232 -1 O LEU A 228 N ILE A 216 SHEET 3 AA4 3 VAL A 329 VAL A 331 -1 O ARG A 330 N VAL A 229 SHEET 1 AA5 2 PHE A 246 ARG A 249 0 SHEET 2 AA5 2 VAL A 252 HIS A 255 -1 O TYR A 254 N PHE A 247 LINK O ALA A 162 MG MG A 501 1555 1555 2.34 LINK O THR A 239 NA NA A 504 1555 1555 2.54 LINK OE1 GLU A 244 NA NA A 504 1555 1555 2.47 LINK O HIS A 267 NA NA A 503 1555 1555 2.15 LINK O ASP A 284 MG MG A 501 1555 1555 2.27 LINK OD1 ASP A 284 MG MG A 501 1555 1555 2.32 LINK OD1 ASP A 284 MG MG A 502 1555 1555 2.16 LINK OG1 THR A 288 MG MG A 501 1555 1555 2.30 LINK MG MG A 501 O1A ADP A 505 1555 1555 2.30 LINK MG MG A 502 O1B ADP A 505 1555 1555 2.03 LINK MG MG A 502 O1A ADP A 505 1555 1555 2.06 LINK MG MG A 502 O HOH A 717 1555 1555 2.11 LINK MG MG A 502 O HOH A 718 1555 1555 2.15 LINK MG MG A 502 O HOH A 850 1555 1555 2.06 LINK NA NA A 503 O1 EDO A 508 1555 1555 2.62 LINK NA NA A 503 O HOH A 735 1555 1555 2.34 LINK NA NA A 503 O HOH A 816 1555 1555 2.26 LINK NA NA A 503 O HOH A 823 1555 1555 2.44 LINK NA NA A 503 O HOH A 851 1555 1555 2.49 LINK NA NA A 504 O3B ADP A 505 1555 1555 2.52 LINK NA NA A 504 O HOH A 787 1555 1555 2.41 LINK NA NA A 504 O HOH A 789 1555 1555 2.62 SITE 1 AC1 5 ALA A 162 ASP A 284 THR A 288 MG A 502 SITE 2 AC1 5 ADP A 505 SITE 1 AC2 6 ASP A 284 MG A 501 ADP A 505 HOH A 717 SITE 2 AC2 6 HOH A 718 HOH A 850 SITE 1 AC3 6 HIS A 267 EDO A 508 HOH A 735 HOH A 816 SITE 2 AC3 6 HOH A 823 HOH A 851 SITE 1 AC4 5 THR A 239 GLU A 244 ADP A 505 HOH A 787 SITE 2 AC4 5 HOH A 789 SITE 1 AC5 27 ALA A 96 PHE A 97 ASN A 98 LEU A 101 SITE 2 AC5 27 ASP A 159 GLY A 161 ALA A 162 LYS A 165 SITE 3 AC5 27 SER A 240 GLU A 244 HIS A 256 ILE A 257 SITE 4 AC5 27 ILE A 258 ASP A 284 THR A 288 MG A 501 SITE 5 AC5 27 MG A 502 NA A 504 HOH A 717 HOH A 718 SITE 6 AC5 27 HOH A 733 HOH A 751 HOH A 803 HOH A 811 SITE 7 AC5 27 HOH A 826 HOH A 836 HOH A 850 SITE 1 AC6 5 PHE A 276 GLY A 307 ASP A 309 HOH A 828 SITE 2 AC6 5 HOH A 841 SITE 1 AC7 3 TYR A 295 ALA A 321 SER A 322 SITE 1 AC8 6 HIS A 267 ASP A 269 LEU A 293 NA A 503 SITE 2 AC8 6 HOH A 612 HOH A 735 SITE 1 AC9 4 ARG A 24 LEU A 185 LYS A 198 ASN A 213 SITE 1 AD1 7 SER A 27 LYS A 28 ALA A 180 LEU A 181 SITE 2 AD1 7 ASP A 182 HOH A 723 HOH A 809 CRYST1 116.830 46.814 57.501 90.00 102.22 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 0.008559 0.000000 0.001855 0.00000 SCALE2 0.000000 0.021361 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017795 0.00000