HEADER TRANSFERASE 19-DEC-14 4XDT TITLE CRYSTAL STRUCTURE OF TREPONEMA PALLIDUM TP0796 FLAVIN TRAFFICKING TITLE 2 PROTEIN, A BIFUNCTIONAL FMN TRANSFERASE/FAD PYROPHOSPHATASE, N55Y TITLE 3 MUTANT, FAD 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 1 14-OCT-15 4XDT 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 53263 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 : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2701 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 28.5396 - 3.8722 0.96 2680 140 0.1632 0.1838 REMARK 3 2 3.8722 - 3.0747 1.00 2737 140 0.1610 0.1958 REMARK 3 3 3.0747 - 2.6864 1.00 2757 124 0.1641 0.1914 REMARK 3 4 2.6864 - 2.4409 1.00 2694 157 0.1579 0.1706 REMARK 3 5 2.4409 - 2.2660 1.00 2699 140 0.1467 0.1709 REMARK 3 6 2.2660 - 2.1325 1.00 2679 149 0.1524 0.1695 REMARK 3 7 2.1325 - 2.0257 1.00 2697 140 0.1543 0.2155 REMARK 3 8 2.0257 - 1.9375 1.00 2717 135 0.1537 0.1679 REMARK 3 9 1.9375 - 1.8630 1.00 2647 149 0.1662 0.1869 REMARK 3 10 1.8630 - 1.7987 1.00 2692 146 0.1718 0.2388 REMARK 3 11 1.7987 - 1.7425 1.00 2696 125 0.1793 0.2442 REMARK 3 12 1.7425 - 1.6926 1.00 2683 153 0.1761 0.2121 REMARK 3 13 1.6926 - 1.6481 1.00 2710 143 0.1781 0.2310 REMARK 3 14 1.6481 - 1.6079 1.00 2659 150 0.1931 0.2388 REMARK 3 15 1.6079 - 1.5713 1.00 2709 130 0.1974 0.2294 REMARK 3 16 1.5713 - 1.5379 1.00 2654 163 0.2098 0.2302 REMARK 3 17 1.5379 - 1.5071 0.99 2615 147 0.2226 0.2433 REMARK 3 18 1.5071 - 1.4787 0.96 2579 143 0.2499 0.2819 REMARK 3 19 1.4787 - 1.4523 0.84 2258 127 0.2630 0.2724 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) : 19.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.14 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 : 0.024 2724 REMARK 3 ANGLE : 1.314 3672 REMARK 3 CHIRALITY : 0.078 422 REMARK 3 PLANARITY : 0.006 469 REMARK 3 DIHEDRAL : 14.065 978 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.6260 47.0098 -0.4713 REMARK 3 T TENSOR REMARK 3 T11: 0.0716 T22: 0.1692 REMARK 3 T33: 0.1183 T12: 0.0039 REMARK 3 T13: -0.0071 T23: 0.0094 REMARK 3 L TENSOR REMARK 3 L11: 1.1678 L22: 1.5280 REMARK 3 L33: 3.4227 L12: 0.2821 REMARK 3 L13: 0.0244 L23: -0.4359 REMARK 3 S TENSOR REMARK 3 S11: 0.0574 S12: 0.0295 S13: 0.0404 REMARK 3 S21: -0.0354 S22: -0.0753 S23: 0.0275 REMARK 3 S31: 0.0415 S32: 0.2265 S33: 0.0620 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 31 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.7733 50.0218 16.7279 REMARK 3 T TENSOR REMARK 3 T11: 0.2306 T22: 0.1399 REMARK 3 T33: 0.1554 T12: 0.0087 REMARK 3 T13: 0.0250 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 1.3075 L22: 0.8054 REMARK 3 L33: 1.5289 L12: 0.4170 REMARK 3 L13: -0.8253 L23: -0.6011 REMARK 3 S TENSOR REMARK 3 S11: 0.2022 S12: -0.1455 S13: 0.1338 REMARK 3 S21: 0.3472 S22: -0.0817 S23: 0.0689 REMARK 3 S31: -0.3349 S32: 0.0430 S33: -0.0711 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 195 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.6078 41.8598 19.5535 REMARK 3 T TENSOR REMARK 3 T11: 0.1468 T22: 0.1376 REMARK 3 T33: 0.1160 T12: 0.0003 REMARK 3 T13: 0.0087 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.5482 L22: 1.1676 REMARK 3 L33: 0.9267 L12: -0.2399 REMARK 3 L13: -0.2615 L23: -0.0667 REMARK 3 S TENSOR REMARK 3 S11: -0.0724 S12: -0.1361 S13: -0.0088 REMARK 3 S21: 0.2902 S22: 0.0406 S23: 0.0936 REMARK 3 S31: 0.0488 S32: -0.0258 S33: 0.0260 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 196 THROUGH 244 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.5684 31.7755 0.1861 REMARK 3 T TENSOR REMARK 3 T11: 0.1389 T22: 0.1664 REMARK 3 T33: 0.1531 T12: 0.0054 REMARK 3 T13: -0.0172 T23: -0.0124 REMARK 3 L TENSOR REMARK 3 L11: 1.1597 L22: 2.4185 REMARK 3 L33: 2.3989 L12: 0.2032 REMARK 3 L13: -0.0173 L23: -1.0612 REMARK 3 S TENSOR REMARK 3 S11: 0.0773 S12: -0.0812 S13: -0.0583 REMARK 3 S21: -0.0823 S22: -0.0848 S23: -0.1158 REMARK 3 S31: 0.2030 S32: 0.2654 S33: 0.0512 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 245 THROUGH 340 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.4287 25.1124 10.1296 REMARK 3 T TENSOR REMARK 3 T11: 0.1246 T22: 0.1168 REMARK 3 T33: 0.1534 T12: -0.0051 REMARK 3 T13: -0.0131 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.0677 L22: 2.0862 REMARK 3 L33: 0.8477 L12: -0.3737 REMARK 3 L13: -0.5525 L23: 0.3165 REMARK 3 S TENSOR REMARK 3 S11: -0.0136 S12: -0.0134 S13: -0.0986 REMARK 3 S21: 0.0996 S22: -0.0255 S23: 0.1273 REMARK 3 S31: 0.0974 S32: 0.0182 S33: 0.0370 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 4XDT 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_1000205498. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-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) : 0.97934 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 : 53283 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 4IFU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 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 58.38850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.49600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.38850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.49600 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 535 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 599 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 O HOH A 683 O HOH A 684 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 70 -147.61 -119.72 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 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 125 OE2 REMARK 620 2 THR A 128 OG1 102.0 REMARK 620 3 HOH A 563 O 133.4 105.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 162 O REMARK 620 2 ASP A 284 O 88.3 REMARK 620 3 ASP A 284 OD1 80.6 89.2 REMARK 620 4 THR A 288 OG1 108.0 93.5 171.1 REMARK 620 5 FAD A 401 O1A 99.0 170.2 85.5 90.6 REMARK 620 6 HOH A 670 O 154.1 101.3 75.6 95.5 69.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 267 O REMARK 620 2 HOH A 708 O 167.1 REMARK 620 3 HOH A 619 O 98.6 94.0 REMARK 620 4 HOH A 668 O 91.9 75.6 169.3 REMARK 620 5 HOH A 700 O 91.4 93.7 80.0 98.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 284 OD1 REMARK 620 2 FAD A 401 O1A 89.9 REMARK 620 3 FAD A 401 O1P 178.0 89.1 REMARK 620 4 HOH A 670 O 75.8 70.0 105.4 REMARK 620 5 HOH A 601 O 89.1 172.3 92.2 102.3 REMARK 620 6 HOH A 607 O 82.6 99.1 95.9 155.6 88.4 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 FAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 414 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 4XDT A 1 340 UNP O83774 APBE_TREPA 23 362 SEQADV 4XDT TYR A 55 UNP O83774 ASN 77 ENGINEERED MUTATION SEQADV 4XDT 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 FAD A 401 84 HET MG A 402 1 HET MG A 403 1 HET NA A 404 1 HET NA A 405 1 HET ACT A 406 7 HET ACT A 407 7 HET ACT A 408 7 HET ACT A 409 7 HET EDO A 410 10 HET EDO A 411 10 HET EDO A 412 10 HET EDO A 413 10 HET EDO A 414 10 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 MG 2(MG 2+) FORMUL 5 NA 2(NA 1+) FORMUL 7 ACT 4(C2 H3 O2 1-) FORMUL 11 EDO 5(C2 H6 O2) FORMUL 16 HOH *208(H2 O) HELIX 1 AA1 PRO A 30 SER A 53 1 24 HELIX 2 AA2 SER A 59 ALA A 66 1 8 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 LEU A 195 N ALA A 184 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 HIS A 136 O GLN A 150 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 ILE A 216 0 SHEET 2 AA4 3 LEU A 228 VAL A 232 -1 O VAL A 232 N TRP A 212 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 OE2 GLU A 125 NA NA A 404 1555 1555 2.39 LINK OG1 THR A 128 NA NA A 404 1555 1555 3.07 LINK O ALA A 162 MG MG A 402 1555 1555 2.44 LINK O HIS A 267 NA NA A 405 1555 1555 2.21 LINK O ASP A 284 MG MG A 402 1555 1555 2.35 LINK OD1 ASP A 284 MG MG A 402 1555 1555 2.34 LINK OD1 ASP A 284 MG MG A 403 1555 1555 2.27 LINK OG1 THR A 288 MG MG A 402 1555 1555 2.30 LINK O1A FAD A 401 MG MG A 402 1555 1555 2.26 LINK O1A FAD A 401 MG MG A 403 1555 1555 2.15 LINK O1P FAD A 401 MG MG A 403 1555 1555 2.16 LINK MG MG A 402 O HOH A 670 1555 1555 2.80 LINK MG MG A 403 O HOH A 670 1555 1555 2.84 LINK MG MG A 403 O HOH A 601 1555 1555 2.06 LINK MG MG A 403 O HOH A 607 1555 1555 2.85 LINK NA NA A 405 O HOH A 708 1555 1555 2.10 LINK NA NA A 405 O HOH A 619 1555 1555 2.28 LINK NA NA A 405 O HOH A 668 1555 1555 2.52 LINK NA NA A 405 O HOH A 700 1555 1555 2.60 LINK NA NA A 404 O HOH A 563 1555 4546 2.20 SITE 1 AC1 28 ILE A 17 GLY A 18 TYR A 55 ALA A 96 SITE 2 AC1 28 PHE A 97 ASN A 98 LEU A 101 ASP A 159 SITE 3 AC1 28 GLY A 161 ALA A 162 ALA A 164 LYS A 165 SITE 4 AC1 28 SER A 240 GLU A 244 ARG A 245 HIS A 256 SITE 5 AC1 28 ILE A 257 ILE A 258 ASP A 284 THR A 288 SITE 6 AC1 28 MG A 402 MG A 403 HOH A 601 HOH A 606 SITE 7 AC1 28 HOH A 670 HOH A 671 HOH A 688 HOH A 705 SITE 1 AC2 6 ALA A 162 ASP A 284 THR A 288 FAD A 401 SITE 2 AC2 6 MG A 403 HOH A 670 SITE 1 AC3 7 LYS A 165 ASP A 284 FAD A 401 MG A 402 SITE 2 AC3 7 HOH A 601 HOH A 607 HOH A 670 SITE 1 AC4 5 GLU A 125 THR A 128 GLY A 140 VAL A 141 SITE 2 AC4 5 HOH A 563 SITE 1 AC5 5 HIS A 267 HOH A 619 HOH A 668 HOH A 700 SITE 2 AC5 5 HOH A 708 SITE 1 AC6 7 SER A 27 LYS A 28 ALA A 180 LEU A 181 SITE 2 AC6 7 ASP A 182 HOH A 612 HOH A 692 SITE 1 AC7 5 ASP A 182 GLY A 196 ASP A 234 ARG A 303 SITE 2 AC7 5 HOH A 555 SITE 1 AC8 4 ARG A 24 LEU A 185 LYS A 198 ASN A 213 SITE 1 AC9 7 GLY A 190 ILE A 192 GLY A 215 ILE A 216 SITE 2 AC9 7 VAL A 237 THR A 239 HOH A 656 SITE 1 AD1 6 CYS A 235 PHE A 276 ALA A 277 GLY A 307 SITE 2 AD1 6 ASP A 309 EDO A 411 SITE 1 AD2 5 VAL A 232 ARG A 233 CYS A 235 EDO A 410 SITE 2 AD2 5 HOH A 523 SITE 1 AD3 6 VAL A 7 GLU A 9 ALA A 13 LEU A 20 SITE 2 AD3 6 HOH A 501 HOH A 517 SITE 1 AD4 3 ASP A 170 GLN A 174 PRO A 278 SITE 1 AD5 7 GLY A 94 GLY A 95 ALA A 96 ASP A 259 SITE 2 AD5 7 VAL A 261 VAL A 292 HOH A 572 CRYST1 116.777 46.992 57.566 90.00 102.21 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 0.008563 0.000000 0.001853 0.00000 SCALE2 0.000000 0.021280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017773 0.00000 MASTER 442 0 14 11 19 0 31 6 0 0 0 27 END