HEADER HYDROLASE 17-AUG-17 6APH TITLE CRYSTAL STRUCTURE OF ADENOSYLHOMOCYSTEINASE FROM ELIZABETHKINGIA TITLE 2 ANOPHELIS NUHP1 IN COMPLEX WITH NAD AND ADENOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENOSYLHOMOCYSTEINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ELANA.00032.A.B1; COMPND 5 SYNONYM: S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE,ADOHCYASE; COMPND 6 EC: 3.3.1.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ELIZABETHKINGIA ANOPHELIS NUHP1; SOURCE 3 ORGANISM_TAXID: 1338011; SOURCE 4 GENE: AHCY, BD94_1936; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: ELANA.00032.A.B1 KEYWDS SSGCID, STRUCTURAL GENOMICS, ELIZABETHKINGIA ANOPHELIS, KEYWDS 2 ADENOSYLHOMOCYSTEINASE, AHCY, SEATTLE STRUCTURAL GENOMICS CENTER FOR KEYWDS 3 INFECTIOUS DISEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 2 13-MAR-24 6APH 1 REMARK REVDAT 1 30-AUG-17 6APH 0 JRNL AUTH J.ABENDROTH,S.L.DELKER,D.D.LORIMER,T.E.EDWARDS JRNL TITL CRYSTAL STRUCTURE OF ADENOSYLHOMOCYSTEINASE FROM JRNL TITL 2 ELIZABETHKINGIA ANOPHELIS NUHP1 IN COMPLEX WITH NAD AND JRNL TITL 3 ADENOSINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 63773 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.160 REMARK 3 FREE R VALUE TEST SET COUNT : 2017 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 43.4153 - 3.9758 0.97 4619 153 0.1397 0.1511 REMARK 3 2 3.9758 - 3.1560 0.98 4456 130 0.1334 0.1618 REMARK 3 3 3.1560 - 2.7572 0.99 4434 152 0.1439 0.1574 REMARK 3 4 2.7572 - 2.5051 0.99 4414 127 0.1514 0.1796 REMARK 3 5 2.5051 - 2.3256 0.99 4412 145 0.1454 0.1452 REMARK 3 6 2.3256 - 2.1885 1.00 4401 149 0.1493 0.1859 REMARK 3 7 2.1885 - 2.0789 1.00 4420 122 0.1514 0.1839 REMARK 3 8 2.0789 - 1.9884 1.00 4394 137 0.1551 0.1827 REMARK 3 9 1.9884 - 1.9118 1.00 4365 152 0.1469 0.1759 REMARK 3 10 1.9118 - 1.8458 1.00 4360 145 0.1521 0.1722 REMARK 3 11 1.8458 - 1.7881 1.00 4398 138 0.1649 0.1748 REMARK 3 12 1.7881 - 1.7370 1.00 4358 160 0.1805 0.2212 REMARK 3 13 1.7370 - 1.6913 1.00 4374 145 0.1958 0.2228 REMARK 3 14 1.6913 - 1.6500 1.00 4351 162 0.2044 0.2689 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) : 14.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.71 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 : 0.009 3546 REMARK 3 ANGLE : 1.037 4854 REMARK 3 CHIRALITY : 0.069 555 REMARK 3 PLANARITY : 0.007 660 REMARK 3 DIHEDRAL : 15.773 2156 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 6 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.4943 36.1815 12.3412 REMARK 3 T TENSOR REMARK 3 T11: 0.2505 T22: 0.3614 REMARK 3 T33: 0.2156 T12: 0.0176 REMARK 3 T13: 0.0539 T23: 0.1066 REMARK 3 L TENSOR REMARK 3 L11: 1.2972 L22: 2.5535 REMARK 3 L33: 2.3901 L12: -0.1069 REMARK 3 L13: 0.9710 L23: -0.2676 REMARK 3 S TENSOR REMARK 3 S11: -0.1025 S12: -0.4781 S13: -0.1958 REMARK 3 S21: 0.4681 S22: -0.0420 S23: 0.0859 REMARK 3 S31: 0.2397 S32: 0.0425 S33: 0.0208 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 46 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.7699 33.1403 10.0190 REMARK 3 T TENSOR REMARK 3 T11: 0.3631 T22: 0.5075 REMARK 3 T33: 0.3291 T12: 0.0986 REMARK 3 T13: -0.0559 T23: 0.1242 REMARK 3 L TENSOR REMARK 3 L11: 1.0625 L22: 1.0629 REMARK 3 L33: 1.4882 L12: -0.0379 REMARK 3 L13: 0.4910 L23: 0.5107 REMARK 3 S TENSOR REMARK 3 S11: -0.0792 S12: -0.4118 S13: -0.2762 REMARK 3 S21: 0.4120 S22: 0.1334 S23: -0.2074 REMARK 3 S31: 0.3890 S32: 0.5049 S33: -0.0469 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.5583 57.7327 -2.0067 REMARK 3 T TENSOR REMARK 3 T11: 0.0889 T22: 0.1643 REMARK 3 T33: 0.1203 T12: -0.0074 REMARK 3 T13: -0.0272 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.7307 L22: 0.6131 REMARK 3 L33: 0.8660 L12: -0.0584 REMARK 3 L13: -0.2074 L23: 0.2444 REMARK 3 S TENSOR REMARK 3 S11: -0.0088 S12: -0.1489 S13: 0.0292 REMARK 3 S21: 0.0765 S22: 0.0422 S23: -0.0820 REMARK 3 S31: 0.0103 S32: 0.0374 S33: -0.0300 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 437 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.5728 28.1637 -10.3901 REMARK 3 T TENSOR REMARK 3 T11: 0.1786 T22: 0.1531 REMARK 3 T33: 0.2255 T12: 0.0081 REMARK 3 T13: -0.0098 T23: 0.0444 REMARK 3 L TENSOR REMARK 3 L11: 1.0298 L22: 0.7650 REMARK 3 L33: 1.7995 L12: -0.0402 REMARK 3 L13: -0.3371 L23: 0.5268 REMARK 3 S TENSOR REMARK 3 S11: -0.0242 S12: -0.1612 S13: -0.2556 REMARK 3 S21: 0.1107 S22: 0.0631 S23: -0.0589 REMARK 3 S31: 0.3093 S32: 0.2076 S33: -0.0507 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 6APH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000229622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-16; 04-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : APS; ROTATING ANODE REMARK 200 BEAMLINE : 21-ID-F; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872; 1.5418 REMARK 200 MONOCHROMATOR : DIAMOND[111]; DIAMOND[111] REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300; RIGAKU SATURN REMARK 200 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63783 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 43.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 10.98 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 11.02 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.660 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER 2.7.17 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RIGAKUREAGENTS SCREEN JCSG+ B5 (40% REMARK 280 MPD, 5% PEG8000, 100 MM SODIUM CACODYLATE / HCL, PH 6.5), 20 MG/ REMARK 280 ML ELANA.00032.A.B1.PS38147 + 2 MM MAGNESIUM CHLORIDE + 2 MM ATP REMARK 280 (ADDED BY MISTAKE DUE TO SAMPLE MIX-UP), CRYOPROTECTION: DIRECT, REMARK 280 PUCK: GLC4-2, FOR PHASING, A CRYSTAL FROM THE SAME WELL WAS REMARK 280 INCUBATED IN 10% ETHYLENE GLYCOL + 5 M POTASSIUM IODIDE (FINAL REMARK 280 CONCENTRATION 500 MM), DATA COLLECTED IN-HOUSE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.26667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.53333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.26667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.53333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 34.26667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 68.53333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.26667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 68.53333 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 28940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.0 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 -1.000000 0.000000 0.000000 -66.29500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 114.82631 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 -34.26667 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 -66.29500 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 114.82631 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -34.26667 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 697 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 744 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 952 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 997 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1012 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 MET A -7 REMARK 465 ALA A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 LYS A 4 REMARK 465 THR A 5 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 GLN A 6 CG CD OE1 NE2 REMARK 470 LYS A 13 CG CD CE NZ REMARK 470 LYS A 49 CG CD CE NZ REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 GLU A 125 CG CD OE1 OE2 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 LYS A 153 CG CD CE NZ REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 GLN A 174 CG CD OE1 NE2 REMARK 470 LYS A 383 CG CD CE NZ REMARK 470 LYS A 405 CG CD CE NZ REMARK 470 LYS A 420 CG CD CE NZ 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 609 O HOH A 839 2.09 REMARK 500 O HOH A 620 O HOH A 688 2.11 REMARK 500 OH TYR A 42 O HOH A 601 2.14 REMARK 500 O HOH A 613 O HOH A 783 2.16 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 1010 O HOH A 1010 12564 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 209 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 58 114.66 -23.66 REMARK 500 ALA A 104 133.87 -170.72 REMARK 500 LYS A 191 -68.30 -102.23 REMARK 500 PHE A 194 -65.65 -122.43 REMARK 500 LYS A 197 -67.86 -91.60 REMARK 500 PHE A 226 42.55 -142.10 REMARK 500 ALA A 355 -138.84 -139.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1020 DISTANCE = 6.07 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: ELANA.00032.A RELATED DB: TARGETTRACK DBREF1 6APH A 1 437 UNP A0A077EDS4_9FLAO DBREF2 6APH A A0A077EDS4 1 437 SEQADV 6APH MET A -7 UNP A0A077EDS EXPRESSION TAG SEQADV 6APH ALA A -6 UNP A0A077EDS EXPRESSION TAG SEQADV 6APH HIS A -5 UNP A0A077EDS EXPRESSION TAG SEQADV 6APH HIS A -4 UNP A0A077EDS EXPRESSION TAG SEQADV 6APH HIS A -3 UNP A0A077EDS EXPRESSION TAG SEQADV 6APH HIS A -2 UNP A0A077EDS EXPRESSION TAG SEQADV 6APH HIS A -1 UNP A0A077EDS EXPRESSION TAG SEQADV 6APH HIS A 0 UNP A0A077EDS EXPRESSION TAG SEQRES 1 A 445 MET ALA HIS HIS HIS HIS HIS HIS MET GLU THR LYS THR SEQRES 2 A 445 GLN TYR VAL PRO TYR LYS VAL LYS ASP ILE SER LEU ALA SEQRES 3 A 445 GLU TRP GLY ARG LYS GLU ILE GLU LEU ALA GLU ALA GLU SEQRES 4 A 445 MET PRO GLY LEU MET ALA ILE ARG GLU GLU TYR GLY PRO SEQRES 5 A 445 GLN GLN PRO LEU LYS GLY ALA ARG ILE ALA GLY CYS LEU SEQRES 6 A 445 HIS MET THR ILE GLN THR ALA VAL LEU ILE GLU THR LEU SEQRES 7 A 445 VAL ALA LEU GLY ALA ASP VAL THR TRP SER SER CYS ASN SEQRES 8 A 445 ILE PHE SER THR GLN ASP HIS ALA ALA ALA ALA ILE ALA SEQRES 9 A 445 ALA ALA GLY ILE PRO VAL TYR ALA TRP LYS GLY MET ASN SEQRES 10 A 445 GLU GLU GLU PHE ASP TRP CYS ILE GLU GLN THR LEU PHE SEQRES 11 A 445 PHE GLY GLU ASP ARG GLN PRO LEU ASN MET ILE LEU ASP SEQRES 12 A 445 ASP GLY GLY ASP LEU THR ASN MET VAL PHE ASP LYS TYR SEQRES 13 A 445 PRO GLU LEU THR LYS ASP ILE LYS GLY LEU SER GLU GLU SEQRES 14 A 445 THR THR THR GLY VAL HIS ARG LEU TYR GLU ARG MET GLN SEQRES 15 A 445 ASN GLY THR LEU VAL MET PRO ALA ILE ASN VAL ASN ASP SEQRES 16 A 445 SER VAL THR LYS SER LYS PHE ASP ASN LYS TYR GLY CYS SEQRES 17 A 445 ARG GLU SER ALA VAL ASP ALA ILE ARG ARG ALA THR ASP SEQRES 18 A 445 VAL MET LEU ALA GLY LYS ARG VAL VAL VAL CYS GLY PHE SEQRES 19 A 445 GLY ASP VAL GLY LYS GLY THR ALA ALA SER PHE ARG GLY SEQRES 20 A 445 ALA GLY SER ILE VAL THR VAL THR GLU ILE ASP PRO ILE SEQRES 21 A 445 CYS ALA LEU GLN ALA ALA MET GLU GLY TYR GLU VAL LYS SEQRES 22 A 445 GLN LEU ASP THR VAL VAL ASP ASN ALA ASP ILE ILE ILE SEQRES 23 A 445 THR THR THR GLY ASN PHE GLY ILE VAL ARG GLY GLU HIS SEQRES 24 A 445 PHE GLU LYS MET LYS ASP LYS THR ILE VAL CYS ASN ILE SEQRES 25 A 445 GLY HIS PHE ASP ASN GLU ILE ASP MET ALA TRP LEU ASN SEQRES 26 A 445 LYS ASN HIS GLY ALA THR LYS VAL GLU ILE LYS PRO GLN SEQRES 27 A 445 VAL ASP LYS TYR ASN VAL ASN GLY ASN ASP ILE ILE ILE SEQRES 28 A 445 LEU ALA GLU GLY ARG LEU VAL ASN LEU GLY CYS ALA THR SEQRES 29 A 445 GLY HIS PRO SER PHE VAL MET SER ASN SER PHE SER ASN SEQRES 30 A 445 GLN THR LEU ALA GLN ILE GLU LEU TRP VAL HIS SER ASP SEQRES 31 A 445 LYS TYR GLU ASN LYS VAL TYR THR LEU PRO LYS HIS LEU SEQRES 32 A 445 ASP GLU LYS VAL ALA ALA LEU HIS LEU LYS LYS LEU GLY SEQRES 33 A 445 VAL GLU LEU GLU THR LEU SER GLU GLU GLN ALA LYS TYR SEQRES 34 A 445 ILE GLY VAL THR VAL ASP GLY PRO PHE LYS PRO ASP TYR SEQRES 35 A 445 TYR ARG TYR HET NAD A 500 44 HET ADN A 501 19 HET MPD A 502 8 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM ADN ADENOSINE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 ADN C10 H13 N5 O4 FORMUL 4 MPD C6 H14 O2 FORMUL 5 HOH *420(H2 O) HELIX 1 AA1 ASP A 14 SER A 16 5 3 HELIX 2 AA2 LEU A 17 GLU A 31 1 15 HELIX 3 AA3 MET A 32 GLY A 43 1 12 HELIX 4 AA4 PRO A 44 GLN A 46 5 3 HELIX 5 AA5 THR A 60 LEU A 73 1 14 HELIX 6 AA6 GLN A 88 ALA A 98 1 11 HELIX 7 AA7 ASN A 109 LEU A 121 1 13 HELIX 8 AA8 GLY A 138 TYR A 148 1 11 HELIX 9 AA9 PRO A 149 ILE A 155 5 7 HELIX 10 AB1 THR A 162 ASN A 175 1 14 HELIX 11 AB2 SER A 188 LYS A 193 1 6 HELIX 12 AB3 PHE A 194 ASP A 213 1 20 HELIX 13 AB4 GLY A 227 GLY A 239 1 13 HELIX 14 AB5 ASP A 250 GLU A 260 1 11 HELIX 15 AB6 GLN A 266 VAL A 271 1 6 HELIX 16 AB7 ASP A 272 ALA A 274 5 3 HELIX 17 AB8 ARG A 288 GLU A 293 1 6 HELIX 18 AB9 PHE A 307 ILE A 311 5 5 HELIX 19 AC1 ASP A 312 GLY A 321 1 10 HELIX 20 AC2 ALA A 322 LYS A 324 5 3 HELIX 21 AC3 GLU A 346 ARG A 348 5 3 HELIX 22 AC4 LEU A 349 ALA A 355 1 7 HELIX 23 AC5 PRO A 359 SER A 381 1 23 HELIX 24 AC6 ASP A 382 TYR A 384 5 3 HELIX 25 AC7 PRO A 392 HIS A 403 1 12 HELIX 26 AC8 LEU A 404 GLY A 408 5 5 HELIX 27 AC9 SER A 415 GLY A 423 1 9 SHEET 1 AA1 7 VAL A 102 TYR A 103 0 SHEET 2 AA1 7 ASP A 76 SER A 80 1 N TRP A 79 O TYR A 103 SHEET 3 AA1 7 ARG A 52 CYS A 56 1 N ILE A 53 O ASP A 76 SHEET 4 AA1 7 MET A 132 ASP A 135 1 O LEU A 134 N CYS A 56 SHEET 5 AA1 7 LEU A 158 GLU A 160 1 O SER A 159 N ASP A 135 SHEET 6 AA1 7 ALA A 182 ASN A 184 1 O ILE A 183 N GLU A 160 SHEET 7 AA1 7 VAL A 388 TYR A 389 1 O TYR A 389 N ASN A 184 SHEET 1 AA2 2 PHE A 122 PHE A 123 0 SHEET 2 AA2 2 GLN A 128 PRO A 129 -1 O GLN A 128 N PHE A 123 SHEET 1 AA3 8 GLU A 263 VAL A 264 0 SHEET 2 AA3 8 ILE A 243 THR A 247 1 N VAL A 246 O GLU A 263 SHEET 3 AA3 8 ARG A 220 CYS A 224 1 N VAL A 223 O THR A 245 SHEET 4 AA3 8 ILE A 276 THR A 279 1 O ILE A 278 N CYS A 224 SHEET 5 AA3 8 THR A 299 ASN A 303 1 O ILE A 300 N ILE A 277 SHEET 6 AA3 8 ASN A 339 LEU A 344 1 O ILE A 342 N VAL A 301 SHEET 7 AA3 8 VAL A 331 VAL A 336 -1 N VAL A 336 O ASN A 339 SHEET 8 AA3 8 VAL A 325 LYS A 328 -1 N VAL A 325 O LYS A 333 CISPEP 1 GLY A 428 PRO A 429 0 8.16 SITE 1 AC1 32 THR A 162 THR A 163 THR A 164 ASN A 196 SITE 2 AC1 32 GLY A 225 GLY A 227 ASP A 228 VAL A 229 SITE 3 AC1 32 THR A 247 GLU A 248 ILE A 249 ASP A 250 SITE 4 AC1 32 CYS A 253 THR A 280 THR A 281 GLY A 282 SITE 5 AC1 32 ASN A 283 ILE A 286 ILE A 304 GLY A 305 SITE 6 AC1 32 HIS A 306 ASN A 351 HIS A 358 LYS A 431 SITE 7 AC1 32 TYR A 435 ADN A 501 HOH A 640 HOH A 656 SITE 8 AC1 32 HOH A 687 HOH A 760 HOH A 838 HOH A 887 SITE 1 AC2 16 LEU A 57 HIS A 58 THR A 60 GLN A 62 SITE 2 AC2 16 THR A 63 ASP A 136 GLU A 161 THR A 162 SITE 3 AC2 16 LYS A 191 ASP A 195 HIS A 306 THR A 356 SITE 4 AC2 16 GLY A 357 HIS A 358 MET A 363 NAD A 500 SITE 1 AC3 2 GLU A 417 LYS A 420 CRYST1 132.590 132.590 102.800 90.00 90.00 120.00 P 64 2 2 12 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 0.007542 0.004354 0.000000 0.00000 SCALE2 0.000000 0.008709 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009728 0.00000