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 2 27-SEP-23 4XDT 1 REMARK LINK 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 619 O 98.6 REMARK 620 3 HOH A 668 O 91.9 169.3 REMARK 620 4 HOH A 700 O 91.4 80.0 98.3 REMARK 620 5 HOH A 708 O 167.1 94.0 75.6 93.7 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 601 O 89.1 172.3 92.2 REMARK 620 5 HOH A 607 O 82.6 99.1 95.9 88.4 REMARK 620 6 HOH A 670 O 75.8 70.0 105.4 102.3 155.6 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 601 1555 1555 2.06 LINK MG MG A 403 O HOH A 607 1555 1555 2.85 LINK MG MG A 403 O HOH A 670 1555 1555 2.84 LINK NA NA A 404 O HOH A 563 1555 4546 2.20 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 405 O HOH A 708 1555 1555 2.10 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