HEADER LYASE 14-DEC-18 6NDN TITLE CRYSTAL STRUCTURE OF SELENOCYSTEINE LYASE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE DESULFURASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SELENOCYSTEINE BETA-LYASE,SCL,SELENOCYSTEINE LYASE, COMPND 5 SELENOCYSTEINE REDUCTASE; COMPND 6 EC: 2.8.1.7,4.4.1.16; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI UMEA 3718-1; SOURCE 3 ORGANISM_TAXID: 1281269; SOURCE 4 GENE: SUFS, G994_01747; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SELENOCYSTEINE LYASE, ENZYME, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.F.SCORTECCI,J.BRANDAO-NETO,H.M.PEREIRA,O.H.THIEMANN REVDAT 2 11-OCT-23 6NDN 1 LINK REVDAT 1 25-DEC-19 6NDN 0 JRNL AUTH J.F.SCORTECCI,J.BRANDAO-NETO,H.M.PEREIRA,O.H.THIEMANN JRNL TITL CRYSTAL STRUCTURE OF SELENOCYSTEINE LYASE FROM ESCHERICHIA JRNL TITL 2 COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 106039 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 5074 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 57.2427 - 5.4926 1.00 3649 195 0.1574 0.1734 REMARK 3 2 5.4926 - 4.3601 1.00 3491 172 0.1217 0.1226 REMARK 3 3 4.3601 - 3.8091 1.00 3439 186 0.1243 0.1390 REMARK 3 4 3.8091 - 3.4609 1.00 3429 183 0.1362 0.1547 REMARK 3 5 3.4609 - 3.2128 1.00 3382 194 0.1650 0.1762 REMARK 3 6 3.2128 - 3.0234 1.00 3385 168 0.1808 0.1811 REMARK 3 7 3.0234 - 2.8720 1.00 3420 147 0.1841 0.1754 REMARK 3 8 2.8720 - 2.7470 1.00 3378 156 0.1881 0.2056 REMARK 3 9 2.7470 - 2.6412 1.00 3391 176 0.1803 0.2337 REMARK 3 10 2.6412 - 2.5501 1.00 3401 144 0.1686 0.2020 REMARK 3 11 2.5501 - 2.4704 1.00 3364 161 0.1689 0.1745 REMARK 3 12 2.4704 - 2.3997 1.00 3388 155 0.1631 0.1961 REMARK 3 13 2.3997 - 2.3366 1.00 3342 162 0.1572 0.1613 REMARK 3 14 2.3366 - 2.2796 1.00 3317 188 0.1547 0.1901 REMARK 3 15 2.2796 - 2.2277 1.00 3348 187 0.1552 0.1511 REMARK 3 16 2.2277 - 2.1803 1.00 3333 171 0.1540 0.1632 REMARK 3 17 2.1803 - 2.1367 1.00 3347 187 0.1542 0.1737 REMARK 3 18 2.1367 - 2.0964 1.00 3334 149 0.1585 0.1724 REMARK 3 19 2.0964 - 2.0589 1.00 3353 165 0.1730 0.2007 REMARK 3 20 2.0589 - 2.0240 1.00 3343 190 0.1769 0.1891 REMARK 3 21 2.0240 - 1.9914 1.00 3298 176 0.1741 0.1933 REMARK 3 22 1.9914 - 1.9607 1.00 3331 178 0.1755 0.1991 REMARK 3 23 1.9607 - 1.9319 1.00 3328 186 0.1827 0.2241 REMARK 3 24 1.9319 - 1.9047 1.00 3311 175 0.1867 0.1774 REMARK 3 25 1.9047 - 1.8790 1.00 3367 142 0.1947 0.1959 REMARK 3 26 1.8790 - 1.8546 1.00 3347 150 0.2068 0.2221 REMARK 3 27 1.8546 - 1.8314 1.00 3298 146 0.2219 0.2256 REMARK 3 28 1.8314 - 1.8093 1.00 3341 165 0.2396 0.2552 REMARK 3 29 1.8093 - 1.7883 1.00 3316 157 0.2698 0.2546 REMARK 3 30 1.7883 - 1.7682 0.95 3194 163 0.2734 0.2783 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 3264 REMARK 3 ANGLE : 1.410 4462 REMARK 3 CHIRALITY : 0.110 503 REMARK 3 PLANARITY : 0.009 581 REMARK 3 DIHEDRAL : 12.237 1939 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.4614 55.2677 5.3570 REMARK 3 T TENSOR REMARK 3 T11: 0.2698 T22: 0.2496 REMARK 3 T33: 0.2752 T12: -0.0657 REMARK 3 T13: -0.0342 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 2.4321 L22: 1.7467 REMARK 3 L33: 0.9432 L12: -0.8129 REMARK 3 L13: -0.7457 L23: 1.1398 REMARK 3 S TENSOR REMARK 3 S11: -0.0030 S12: -0.1565 S13: 0.4163 REMARK 3 S21: 0.0689 S22: 0.1116 S23: -0.2617 REMARK 3 S31: -0.1407 S32: 0.1249 S33: -0.1102 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 60 THROUGH 298 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.5240 37.0203 12.8014 REMARK 3 T TENSOR REMARK 3 T11: 0.2475 T22: 0.2497 REMARK 3 T33: 0.2222 T12: -0.0228 REMARK 3 T13: -0.0071 T23: 0.0410 REMARK 3 L TENSOR REMARK 3 L11: 1.0339 L22: 0.7933 REMARK 3 L33: 0.7666 L12: -0.3279 REMARK 3 L13: -0.2588 L23: 0.2195 REMARK 3 S TENSOR REMARK 3 S11: -0.0511 S12: -0.1128 S13: -0.1152 REMARK 3 S21: 0.1389 S22: 0.0174 S23: 0.1071 REMARK 3 S31: 0.0782 S32: -0.0143 S33: 0.0374 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 299 THROUGH 387 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4719 62.5888 7.2854 REMARK 3 T TENSOR REMARK 3 T11: 0.3003 T22: 0.2402 REMARK 3 T33: 0.2774 T12: 0.0295 REMARK 3 T13: 0.0118 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 1.8778 L22: 1.6405 REMARK 3 L33: 0.9006 L12: -0.0972 REMARK 3 L13: -0.0139 L23: -0.0386 REMARK 3 S TENSOR REMARK 3 S11: 0.0263 S12: -0.0627 S13: 0.2388 REMARK 3 S21: 0.0808 S22: 0.0391 S23: 0.1585 REMARK 3 S31: -0.2006 S32: -0.1685 S33: -0.0585 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 388 THROUGH 406 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.9917 74.3930 2.8410 REMARK 3 T TENSOR REMARK 3 T11: 0.4198 T22: 0.2030 REMARK 3 T33: 0.4070 T12: 0.0476 REMARK 3 T13: 0.0569 T23: 0.0301 REMARK 3 L TENSOR REMARK 3 L11: 4.2860 L22: 2.6520 REMARK 3 L33: 5.6765 L12: -0.3739 REMARK 3 L13: 2.3511 L23: -0.4576 REMARK 3 S TENSOR REMARK 3 S11: -0.1821 S12: -0.0103 S13: 0.7408 REMARK 3 S21: 0.1052 S22: 0.0047 S23: 0.0476 REMARK 3 S31: -0.7812 S32: -0.2660 S33: 0.1380 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 6NDN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1000238362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96863 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 106193 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.768 REMARK 200 RESOLUTION RANGE LOW (A) : 92.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.80 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 24.70 REMARK 200 R MERGE FOR SHELL (I) : 2.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1JF9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 79.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M SODIUM FORMATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 67.04550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 63.26000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 63.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 100.56825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 63.26000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 63.26000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.52275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 63.26000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.26000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 100.56825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 63.26000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.26000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.52275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 67.04550 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 NA NA A 502 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 822 LIES ON A SPECIAL POSITION. 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 56 CG CD NE CZ NH1 NH2 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 783 O HOH A 968 2.07 REMARK 500 O HOH A 710 O HOH A 920 2.08 REMARK 500 O HOH A 843 O HOH A 868 2.12 REMARK 500 O HOH A 610 O HOH A 949 2.12 REMARK 500 O HOH A 910 O HOH A 919 2.13 REMARK 500 O HOH A 720 O HOH A 927 2.18 REMARK 500 O HOH A 898 O HOH A 979 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 819 O HOH A 819 7555 2.08 REMARK 500 O HOH A 836 O HOH A 964 7555 2.13 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 THR A 2 -47.23 108.98 REMARK 500 VAL A 54 -133.80 -99.49 REMARK 500 ILE A 118 -168.69 -119.97 REMARK 500 ILE A 127 -58.49 -123.89 REMARK 500 LEU A 227 39.81 -98.79 REMARK 500 TRP A 249 -80.31 -109.96 REMARK 500 SER A 254 -26.79 79.66 REMARK 500 ASN A 330 31.02 -88.85 REMARK 500 ALA A 365 59.81 -143.10 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 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 96 OE1 REMARK 620 2 GLU A 96 OE1 0.0 REMARK 620 3 GLU A 250 OE2 86.9 86.9 REMARK 620 4 GLU A 250 OE2 86.9 86.9 0.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 502 DBREF 6NDN A 1 406 UNP T9SRD8 T9SRD8_ECOLX 1 406 SEQRES 1 A 406 MET THR PHE SER VAL ASP LYS VAL ARG ALA ASP PHE PRO SEQRES 2 A 406 VAL LEU SER ARG GLU VAL ASN GLY LEU PRO LEU ALA TYR SEQRES 3 A 406 LEU ASP SER ALA ALA SER ALA GLN LYS PRO SER GLN VAL SEQRES 4 A 406 ILE ASP ALA GLU ALA GLU PHE TYR ARG HIS GLY TYR ALA SEQRES 5 A 406 ALA VAL HIS ARG GLY ILE HIS THR LEU SER ALA GLN ALA SEQRES 6 A 406 THR GLU LYS MET GLU ASN VAL ARG LYS ARG ALA SER LEU SEQRES 7 A 406 PHE ILE ASN ALA ARG SER ALA GLU GLU LEU VAL PHE VAL SEQRES 8 A 406 ARG GLY THR THR GLU GLY ILE ASN LEU VAL ALA ASN SER SEQRES 9 A 406 TRP GLY ASN SER ASN VAL ARG ALA GLY ASP ASN ILE ILE SEQRES 10 A 406 ILE SER GLN MET GLU HIS HIS ALA ASN ILE VAL PRO TRP SEQRES 11 A 406 GLN MET LEU CYS ALA ARG VAL GLY ALA GLU LEU ARG VAL SEQRES 12 A 406 ILE PRO LEU ASN PRO ASP GLY THR LEU GLN LEU GLU THR SEQRES 13 A 406 LEU PRO THR LEU PHE ASP GLU LYS THR ARG LEU LEU ALA SEQRES 14 A 406 ILE THR HIS VAL SER ASN VAL LEU GLY THR GLU ASN PRO SEQRES 15 A 406 LEU ALA GLU MET ILE THR LEU ALA HIS GLN HIS GLY ALA SEQRES 16 A 406 LYS VAL LEU VAL ASP GLY ALA GLN ALA VAL MET HIS HIS SEQRES 17 A 406 PRO VAL ASP VAL GLN ALA LEU ASP CYS ASP PHE TYR VAL SEQRES 18 A 406 PHE SER GLY HIS LYS LEU TYR GLY PRO THR GLY ILE GLY SEQRES 19 A 406 ILE LEU TYR VAL LYS GLU ALA LEU LEU GLN GLU MET PRO SEQRES 20 A 406 PRO TRP GLU GLY GLY GLY SER MET ILE ALA THR VAL SER SEQRES 21 A 406 LEU SER GLU GLY THR THR TRP THR LYS ALA PRO TRP ARG SEQRES 22 A 406 PHE GLU ALA GLY THR PRO ASN THR GLY GLY ILE ILE GLY SEQRES 23 A 406 LEU GLY ALA ALA LEU GLU TYR VAL SER ALA LEU GLY LEU SEQRES 24 A 406 ASN ASN ILE ALA GLU TYR GLU GLN ASN LEU MET HIS TYR SEQRES 25 A 406 ALA LEU SER GLN LEU GLU SER VAL PRO ASP LEU THR LEU SEQRES 26 A 406 TYR GLY PRO GLN ASN ARG LEU GLY VAL ILE ALA PHE ASN SEQRES 27 A 406 LEU GLY LYS HIS HIS ALA TYR ASP VAL GLY SER PHE LEU SEQRES 28 A 406 ASP ASN TYR GLY ILE ALA VAL ARG THR GLY HIS HIS CYS SEQRES 29 A 406 ALA MET PRO LEU MET ALA TYR TYR ASN VAL PRO ALA MET SEQRES 30 A 406 CYS ARG ALA SER LEU ALA MET TYR ASN THR HIS GLU GLU SEQRES 31 A 406 VAL ASP ARG LEU VAL THR GLY LEU GLN ARG ILE HIS ARG SEQRES 32 A 406 LEU LEU GLY HET PLP A 501 15 HET NA A 502 1 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM NA SODIUM ION HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 NA NA 1+ FORMUL 4 HOH *406(H2 O) HELIX 1 AA1 SER A 4 ALA A 10 1 7 HELIX 2 AA2 ASP A 11 SER A 16 5 6 HELIX 3 AA3 PRO A 36 GLY A 50 1 15 HELIX 4 AA4 HIS A 59 ILE A 80 1 22 HELIX 5 AA5 SER A 84 GLU A 86 5 3 HELIX 6 AA6 GLY A 93 VAL A 110 1 18 HELIX 7 AA7 HIS A 123 ASN A 126 5 4 HELIX 8 AA8 ILE A 127 GLY A 138 1 12 HELIX 9 AA9 GLN A 153 GLU A 155 5 3 HELIX 10 AB1 THR A 156 PHE A 161 1 6 HELIX 11 AB2 PRO A 182 HIS A 193 1 12 HELIX 12 AB3 ASP A 211 ASP A 216 1 6 HELIX 13 AB4 HIS A 225 LEU A 227 5 3 HELIX 14 AB5 LYS A 239 GLN A 244 1 6 HELIX 15 AB6 PRO A 271 GLU A 275 5 5 HELIX 16 AB7 ASN A 280 GLY A 298 1 19 HELIX 17 AB8 GLY A 298 GLU A 318 1 21 HELIX 18 AB9 HIS A 343 TYR A 354 1 12 HELIX 19 AC1 ALA A 365 TYR A 372 1 8 HELIX 20 AC2 THR A 387 GLY A 406 1 20 SHEET 1 AA1 2 GLU A 18 VAL A 19 0 SHEET 2 AA1 2 LEU A 22 PRO A 23 -1 O LEU A 22 N VAL A 19 SHEET 1 AA2 2 ALA A 25 TYR A 26 0 SHEET 2 AA2 2 ILE A 356 ALA A 357 1 O ALA A 357 N ALA A 25 SHEET 1 AA3 7 LEU A 88 VAL A 91 0 SHEET 2 AA3 7 GLY A 234 VAL A 238 -1 O LEU A 236 N VAL A 89 SHEET 3 AA3 7 PHE A 219 SER A 223 -1 N TYR A 220 O TYR A 237 SHEET 4 AA3 7 LYS A 196 ASP A 200 1 N VAL A 199 O PHE A 219 SHEET 5 AA3 7 THR A 165 THR A 171 1 N ILE A 170 O ASP A 200 SHEET 6 AA3 7 ASN A 115 SER A 119 1 N ILE A 117 O ALA A 169 SHEET 7 AA3 7 GLU A 140 ILE A 144 1 O ARG A 142 N ILE A 116 SHEET 1 AA4 2 ILE A 256 SER A 260 0 SHEET 2 AA4 2 GLY A 264 TRP A 267 -1 O THR A 266 N ALA A 257 SHEET 1 AA5 4 LEU A 323 TYR A 326 0 SHEET 2 AA5 4 VAL A 334 LEU A 339 -1 O ASN A 338 N THR A 324 SHEET 3 AA5 4 MET A 377 SER A 381 -1 O CYS A 378 N PHE A 337 SHEET 4 AA5 4 ARG A 359 GLY A 361 -1 N GLY A 361 O MET A 377 LINK NZ LYS A 226 C4A PLP A 501 1555 1555 1.00 LINK OE1 GLU A 96 NA NA A 502 1555 1555 2.36 LINK OE1 GLU A 96 NA NA A 502 1555 7555 2.36 LINK OE2 GLU A 250 NA NA A 502 1555 1555 2.26 LINK OE2 GLU A 250 NA NA A 502 1555 7555 2.26 CISPEP 1 ALA A 270 PRO A 271 0 4.29 SITE 1 AC1 13 THR A 94 THR A 95 HIS A 123 ALA A 125 SITE 2 AC1 13 ASN A 175 ASP A 200 ALA A 202 GLN A 203 SITE 3 AC1 13 SER A 223 HIS A 225 LYS A 226 THR A 278 SITE 4 AC1 13 HOH A 699 SITE 1 AC2 3 GLU A 96 TRP A 249 GLU A 250 CRYST1 126.520 126.520 134.091 90.00 90.00 90.00 P 43 21 2 8 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 0.007904 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007458 0.00000