HEADER OXIDOREDUCTASE 10-JUL-23 8K1H TITLE CRYSTAL STRUCTURE OF ETHYLENE GLYCOL-BOUND GLYCEROL DEHYDROGENASE FROM TITLE 2 KLEBSIELLA PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCEROL DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: GLDA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCEROL DEHYDROGENASE, ETHYLENE GLYCOL, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR W.KANG REVDAT 1 29-MAY-24 8K1H 0 JRNL AUTH G.S.KO,T.Q.NGUYEN,S.KHO,W.KANG JRNL TITL CRYSTAL STRUCTURE OF GLYCEROL DEHYDROGENASE FROM KLEBSIELLA JRNL TITL 2 PNEUMONIAE JRNL REF J. KOREAN CHEM. SOC. V. 68 32 2024 JRNL DOI 10.5012/JKCS.2024.68.1.32 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 40624 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 48.9500 - 5.0600 0.99 2919 152 0.1615 0.1626 REMARK 3 2 5.0600 - 4.0200 1.00 2833 146 0.1341 0.1456 REMARK 3 3 4.0200 - 3.5100 1.00 2777 144 0.1583 0.1580 REMARK 3 4 3.5100 - 3.1900 1.00 2771 143 0.1720 0.1932 REMARK 3 5 3.1900 - 2.9600 1.00 2755 143 0.1904 0.2377 REMARK 3 6 2.9600 - 2.7900 1.00 2750 142 0.1849 0.2195 REMARK 3 7 2.7800 - 2.6500 1.00 2740 142 0.1752 0.2296 REMARK 3 8 2.6500 - 2.5300 1.00 2739 141 0.1769 0.1642 REMARK 3 9 2.5300 - 2.4300 1.00 2730 142 0.1866 0.2356 REMARK 3 10 2.4300 - 2.3500 1.00 2740 142 0.1867 0.1994 REMARK 3 11 2.3500 - 2.2800 1.00 2715 140 0.1857 0.2453 REMARK 3 12 2.2800 - 2.2100 1.00 2745 142 0.1860 0.2686 REMARK 3 13 2.2100 - 2.1500 1.00 2724 141 0.1985 0.2706 REMARK 3 14 2.1500 - 2.1000 0.99 2687 139 0.2076 0.2504 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) : 0.194 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.652 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.67 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 : 0.007 2819 REMARK 3 ANGLE : 0.975 3840 REMARK 3 CHIRALITY : 0.055 450 REMARK 3 PLANARITY : 0.008 496 REMARK 3 DIHEDRAL : 10.789 398 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 37 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.4563 -35.5675 -7.5779 REMARK 3 T TENSOR REMARK 3 T11: 0.2504 T22: 0.1822 REMARK 3 T33: 0.2472 T12: -0.0390 REMARK 3 T13: -0.0207 T23: 0.0138 REMARK 3 L TENSOR REMARK 3 L11: 1.0226 L22: 1.2044 REMARK 3 L33: 2.1907 L12: -0.1172 REMARK 3 L13: -0.3007 L23: 1.1894 REMARK 3 S TENSOR REMARK 3 S11: 0.0778 S12: 0.0079 S13: -0.0647 REMARK 3 S21: -0.0896 S22: 0.0824 S23: -0.1024 REMARK 3 S31: 0.1154 S32: -0.0089 S33: -0.1612 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 38 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.9484 -36.7786 -16.9705 REMARK 3 T TENSOR REMARK 3 T11: 0.2697 T22: 0.2312 REMARK 3 T33: 0.2646 T12: -0.0709 REMARK 3 T13: -0.0582 T23: -0.0317 REMARK 3 L TENSOR REMARK 3 L11: 2.0921 L22: 2.5340 REMARK 3 L33: 1.8707 L12: 0.7217 REMARK 3 L13: 0.0913 L23: 0.3127 REMARK 3 S TENSOR REMARK 3 S11: -0.0616 S12: 0.1381 S13: 0.0361 REMARK 3 S21: -0.1825 S22: 0.0357 S23: 0.1968 REMARK 3 S31: 0.0419 S32: -0.1855 S33: 0.0359 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 248 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.9158 -20.4339 -12.3123 REMARK 3 T TENSOR REMARK 3 T11: 0.2232 T22: 0.2118 REMARK 3 T33: 0.2137 T12: -0.0295 REMARK 3 T13: -0.0509 T23: -0.0216 REMARK 3 L TENSOR REMARK 3 L11: 0.7945 L22: 1.3397 REMARK 3 L33: 0.9996 L12: -0.2229 REMARK 3 L13: -0.3073 L23: 0.3420 REMARK 3 S TENSOR REMARK 3 S11: 0.0070 S12: 0.1257 S13: -0.0929 REMARK 3 S21: -0.1318 S22: -0.0143 S23: 0.1888 REMARK 3 S31: -0.0184 S32: -0.0492 S33: 0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 249 THROUGH 367 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.0672 -5.0835 -22.2034 REMARK 3 T TENSOR REMARK 3 T11: 0.2757 T22: 0.2530 REMARK 3 T33: 0.1958 T12: 0.0039 REMARK 3 T13: -0.0835 T23: -0.0263 REMARK 3 L TENSOR REMARK 3 L11: 2.0987 L22: 2.9610 REMARK 3 L33: 1.9203 L12: -0.8543 REMARK 3 L13: -0.0189 L23: -0.3994 REMARK 3 S TENSOR REMARK 3 S11: 0.0912 S12: 0.2832 S13: -0.0779 REMARK 3 S21: -0.4502 S22: -0.0857 S23: 0.2871 REMARK 3 S31: 0.0063 S32: -0.1633 S33: 0.0026 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 8K1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039342. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40658 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 17.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 5ZXL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6 M AMMONIUM TARTRATE DIBASIC, 0.15 REMARK 280 M SODIUM ACETATE TRIHYDRATE(PH4.6), VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 89.86600 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 89.86600 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 42.46150 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 89.86600 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 89.86600 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 42.46150 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 89.86600 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 89.86600 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 42.46150 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 89.86600 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 89.86600 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 42.46150 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 89.86600 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 89.86600 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 42.46150 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 89.86600 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 89.86600 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 42.46150 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 89.86600 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 89.86600 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 42.46150 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 89.86600 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 89.86600 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 42.46150 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 39920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 92130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -424.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000 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 GLU A 30 CG CD OE1 OE2 REMARK 470 LYS A 38 CG CD CE NZ REMARK 470 GLU A 136 CG CD OE1 OE2 REMARK 470 HIS A 268 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 365 CG CD OE1 OE2 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 ILE A 307 O HOH A 501 1.94 REMARK 500 O HOH A 576 O HOH A 658 1.95 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 ASP A 37 CB - CG - OD1 ANGL. DEV. = 5.8 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 ALA A 118 65.46 -113.52 REMARK 500 ASP A 138 -54.98 -120.11 REMARK 500 THR A 238 -73.13 -111.82 REMARK 500 ALA A 251 -126.73 -148.62 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 171 OD1 REMARK 620 2 HIS A 254 NE2 103.8 REMARK 620 3 HIS A 271 NE2 100.6 117.7 REMARK 620 4 EDO A 403 O1 103.6 87.5 139.3 REMARK 620 N 1 2 3 DBREF 8K1H A 1 367 UNP A6TGD6 A6TGD6_KLEP7 1 367 SEQRES 1 A 367 MET ASP ARG ILE ILE GLN SER PRO GLY LYS TYR ILE GLN SEQRES 2 A 367 GLY THR GLY ALA ILE LYS ARG LEU GLY ASP TYR LEU LYS SEQRES 3 A 367 PRO LEU ALA GLU ARG TRP LEU VAL VAL GLY ASP LYS PHE SEQRES 4 A 367 VAL LEU GLY PHE ALA GLU GLU MET LEU ARG LYS SER LEU SEQRES 5 A 367 ALA ASP ALA GLY LEU ALA ALA GLU ILE ALA PRO PHE GLY SEQRES 6 A 367 GLY GLU CYS SER HIS ASN GLU ILE ASN ARG LEU ARG ASP SEQRES 7 A 367 ILE ALA GLY ASN ALA LYS CYS THR ALA VAL LEU GLY ILE SEQRES 8 A 367 GLY GLY GLY LYS THR LEU ASP THR ALA LYS ALA LEU ALA SEQRES 9 A 367 HIS PHE MET ASN VAL PRO VAL ALA ILE ALA PRO THR ILE SEQRES 10 A 367 ALA SER THR ASP ALA PRO CYS SER ALA LEU SER VAL ILE SEQRES 11 A 367 TYR THR ASP GLU GLY GLU PHE ASP SER TYR LEU MET LEU SEQRES 12 A 367 PRO ARG ASN PRO ASN MET VAL ILE VAL ASP THR GLN ILE SEQRES 13 A 367 VAL ALA GLY ALA PRO ALA ARG LEU LEU ALA ALA GLY ILE SEQRES 14 A 367 GLY ASP ALA LEU ALA THR TRP PHE GLU ALA ARG ALA CYS SEQRES 15 A 367 SER ARG SER GLY ALA THR THR MET ALA GLY GLY LYS CYS SEQRES 16 A 367 THR GLN ALA ALA LEU ALA LEU ALA GLU LEU CYS TYR ASN SEQRES 17 A 367 THR LEU LEU GLU GLU GLY GLU LYS ALA MET LEU ALA ALA SEQRES 18 A 367 GLU GLN HIS VAL VAL THR PRO ALA LEU GLU ARG VAL VAL SEQRES 19 A 367 GLU ALA ASN THR TYR LEU SER GLY VAL GLY PHE GLU SER SEQRES 20 A 367 GLY GLY LEU ALA ALA ALA HIS ALA ILE HIS ASN GLY MET SEQRES 21 A 367 THR ALA ILE PRO ASP ALA HIS HIS TYR TYR HIS GLY GLU SEQRES 22 A 367 LYS VAL ALA PHE GLY THR LEU THR GLN LEU VAL LEU GLU SEQRES 23 A 367 ASN ALA PRO VAL ASP GLU ILE GLU THR VAL ALA ALA LEU SEQRES 24 A 367 CYS HIS SER VAL GLY LEU PRO ILE THR LEU ALA GLN LEU SEQRES 25 A 367 ASP ILE LYS GLY ASP ILE PRO THR LYS MET ARG LEU VAL SEQRES 26 A 367 ALA GLU ALA ALA CYS ALA GLU GLY GLU THR ILE HIS ASN SEQRES 27 A 367 MET PRO GLY GLY VAL ASP SER ASP GLN VAL TYR ALA ALA SEQRES 28 A 367 LEU LEU VAL ALA ASP GLN TYR GLY GLN ARG PHE LEU GLN SEQRES 29 A 367 GLU TRP GLU HET ZN A 401 1 HET NAD A 402 44 HET EDO A 403 4 HET TLA A 404 10 HET TLA A 405 10 HET EDO A 406 4 HETNAM ZN ZINC ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM TLA L(+)-TARTARIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 NAD C21 H27 N7 O14 P2 FORMUL 4 EDO 2(C2 H6 O2) FORMUL 5 TLA 2(C4 H6 O6) FORMUL 8 HOH *254(H2 O) HELIX 1 AA1 GLY A 16 LYS A 19 5 4 HELIX 2 AA2 ARG A 20 LYS A 26 1 7 HELIX 3 AA3 ASP A 37 ALA A 55 1 19 HELIX 4 AA4 SER A 69 ALA A 83 1 15 HELIX 5 AA5 GLY A 93 ASN A 108 1 16 HELIX 6 AA6 ASP A 121 SER A 125 5 5 HELIX 7 AA7 THR A 154 ALA A 160 1 7 HELIX 8 AA8 PRO A 161 GLY A 186 1 26 HELIX 9 AA9 THR A 196 HIS A 224 1 29 HELIX 10 AB1 THR A 227 GLY A 249 1 23 HELIX 11 AB2 ALA A 251 MET A 260 1 10 HELIX 12 AB3 THR A 261 ILE A 263 5 3 HELIX 13 AB4 TYR A 270 GLU A 286 1 17 HELIX 14 AB5 PRO A 289 VAL A 303 1 15 HELIX 15 AB6 LEU A 309 ASP A 313 5 5 HELIX 16 AB7 ASP A 317 CYS A 330 1 14 HELIX 17 AB8 GLU A 334 MET A 339 5 6 HELIX 18 AB9 ASP A 344 TRP A 366 1 23 SHEET 1 AA1 6 LYS A 10 GLY A 14 0 SHEET 2 AA1 6 MET A 149 ASP A 153 1 O VAL A 150 N ILE A 12 SHEET 3 AA1 6 VAL A 111 PRO A 115 1 N ILE A 113 O ILE A 151 SHEET 4 AA1 6 ALA A 87 GLY A 92 1 N GLY A 90 O ALA A 114 SHEET 5 AA1 6 ARG A 31 GLY A 36 1 N LEU A 33 O LEU A 89 SHEET 6 AA1 6 ALA A 58 PRO A 63 1 O ALA A 62 N VAL A 34 SHEET 1 AA2 2 LEU A 127 TYR A 131 0 SHEET 2 AA2 2 PHE A 137 MET A 142 -1 O LEU A 141 N SER A 128 LINK OD1 ASP A 171 ZN ZN A 401 1555 1555 2.08 LINK NE2 HIS A 254 ZN ZN A 401 1555 1555 2.19 LINK NE2 HIS A 271 ZN ZN A 401 1555 1555 2.23 LINK ZN ZN A 401 O1 EDO A 403 1555 1555 1.93 CRYST1 179.732 179.732 84.923 90.00 90.00 90.00 I 4 2 2 16 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 0.005564 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005564 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011775 0.00000 CONECT 1248 2700 CONECT 1849 2700 CONECT 1981 2700 CONECT 2700 1248 1849 1981 2746 CONECT 2701 2702 2703 2704 2723 CONECT 2702 2701 CONECT 2703 2701 CONECT 2704 2701 2705 CONECT 2705 2704 2706 CONECT 2706 2705 2707 2708 CONECT 2707 2706 2712 CONECT 2708 2706 2709 2710 CONECT 2709 2708 CONECT 2710 2708 2711 2712 CONECT 2711 2710 CONECT 2712 2707 2710 2713 CONECT 2713 2712 2714 2722 CONECT 2714 2713 2715 CONECT 2715 2714 2716 CONECT 2716 2715 2717 2722 CONECT 2717 2716 2718 2719 CONECT 2718 2717 CONECT 2719 2717 2720 CONECT 2720 2719 2721 CONECT 2721 2720 2722 CONECT 2722 2713 2716 2721 CONECT 2723 2701 2724 CONECT 2724 2723 2725 2726 2727 CONECT 2725 2724 CONECT 2726 2724 CONECT 2727 2724 2728 CONECT 2728 2727 2729 CONECT 2729 2728 2730 2731 CONECT 2730 2729 2735 CONECT 2731 2729 2732 2733 CONECT 2732 2731 CONECT 2733 2731 2734 2735 CONECT 2734 2733 CONECT 2735 2730 2733 2736 CONECT 2736 2735 2737 2744 CONECT 2737 2736 2738 CONECT 2738 2737 2739 2742 CONECT 2739 2738 2740 2741 CONECT 2740 2739 CONECT 2741 2739 CONECT 2742 2738 2743 CONECT 2743 2742 2744 CONECT 2744 2736 2743 CONECT 2745 2746 2747 CONECT 2746 2700 2745 CONECT 2747 2745 2748 CONECT 2748 2747 CONECT 2749 2751 CONECT 2750 2751 CONECT 2751 2749 2750 2752 CONECT 2752 2751 2753 2754 CONECT 2753 2752 CONECT 2754 2752 2755 2756 CONECT 2755 2754 CONECT 2756 2754 2757 2758 CONECT 2757 2756 CONECT 2758 2756 CONECT 2759 2761 CONECT 2760 2761 CONECT 2761 2759 2760 2762 CONECT 2762 2761 2763 2764 CONECT 2763 2762 CONECT 2764 2762 2765 2766 CONECT 2765 2764 CONECT 2766 2764 2767 2768 CONECT 2767 2766 CONECT 2768 2766 CONECT 2769 2770 2771 CONECT 2770 2769 CONECT 2771 2769 2772 CONECT 2772 2771 MASTER 410 0 6 18 8 0 0 6 3022 1 76 29 END