HEADER HYDROLASE 24-OCT-17 5YNL TITLE CRYSTAL STRUCTURE OF A COLD-ADAPTED ARGINASE FROM PSYCHROPHILIC YEAST, TITLE 2 GLACIOZYMA ANTARCTICA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARGINASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLACIOZYMA ANTARCTICA; SOURCE 3 ORGANISM_TAXID: 105987; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ARGINASE, GLACIOZYMA ANTARCTICA, ENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.Y.YUSOF,D.H.X.QUAY,R.M.ILLIAS,M.FIRDAUS-RAIH,F.D.ABU-BAKAR, AUTHOR 2 N.M.MAHADI,A.M.A.MURAD REVDAT 2 22-NOV-23 5YNL 1 REMARK REVDAT 1 31-JAN-18 5YNL 0 JRNL AUTH A.M.A.MURAD,F.D.ABU-BAKAR,R.M.ILLIAS,N.M.MAHADI, JRNL AUTH 2 M.FIRDAUS-RAIH,D.H.X.QUAY,N.Y.YUSOF JRNL TITL CRYSTAL STRUCTURE OF A COLD-ADAPTED ARGINASE FROM JRNL TITL 2 PSYCHROPHILIC YEAST, GLACIOZYMA ANTARCTICA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 13805 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 692 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 28.7692 - 4.0135 0.98 2661 79 0.1896 0.1895 REMARK 3 2 4.0135 - 3.1869 0.97 2530 172 0.2373 0.2822 REMARK 3 3 3.1869 - 2.7845 1.00 2643 140 0.2436 0.2787 REMARK 3 4 2.7845 - 2.5301 1.00 2659 135 0.2565 0.3060 REMARK 3 5 2.5301 - 2.3488 1.00 2620 166 0.2704 0.3358 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 2080 REMARK 3 ANGLE : 1.321 2833 REMARK 3 CHIRALITY : 0.079 332 REMARK 3 PLANARITY : 0.007 367 REMARK 3 DIHEDRAL : 15.254 739 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 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.9076 24.2714 83.6483 REMARK 3 T TENSOR REMARK 3 T11: 0.6935 T22: 0.3661 REMARK 3 T33: 0.4467 T12: -0.2130 REMARK 3 T13: 0.0084 T23: 0.0526 REMARK 3 L TENSOR REMARK 3 L11: 2.2003 L22: 2.5204 REMARK 3 L33: 4.3490 L12: -0.2011 REMARK 3 L13: 0.1764 L23: 0.3104 REMARK 3 S TENSOR REMARK 3 S11: 0.2999 S12: 0.0594 S13: 0.3463 REMARK 3 S21: -0.5994 S22: -0.0154 S23: -0.2868 REMARK 3 S31: -1.0917 S32: 0.7175 S33: -0.1288 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 126 THROUGH 190 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.1888 10.8527 90.6273 REMARK 3 T TENSOR REMARK 3 T11: 0.2839 T22: 0.8175 REMARK 3 T33: 0.5578 T12: -0.0727 REMARK 3 T13: -0.0716 T23: 0.1047 REMARK 3 L TENSOR REMARK 3 L11: 4.6012 L22: 2.6184 REMARK 3 L33: 1.0885 L12: 0.4941 REMARK 3 L13: 0.0940 L23: -0.4142 REMARK 3 S TENSOR REMARK 3 S11: 0.0486 S12: -0.1374 S13: -0.1166 REMARK 3 S21: -0.0255 S22: -0.1888 S23: -0.8201 REMARK 3 S31: -0.0623 S32: 1.3505 S33: -0.1706 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 191 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.6839 -0.0409 92.1832 REMARK 3 T TENSOR REMARK 3 T11: 0.5714 T22: 1.1122 REMARK 3 T33: 0.7418 T12: 0.2466 REMARK 3 T13: -0.2590 T23: 0.1078 REMARK 3 L TENSOR REMARK 3 L11: 8.5029 L22: 1.8843 REMARK 3 L33: 0.6402 L12: 3.4826 REMARK 3 L13: 1.6876 L23: 1.0653 REMARK 3 S TENSOR REMARK 3 S11: -0.2580 S12: 1.7955 S13: -0.2338 REMARK 3 S21: -0.0856 S22: -0.4254 S23: -0.5803 REMARK 3 S31: 0.0835 S32: 1.0955 S33: 0.3969 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 207 THROUGH 318 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.0468 11.6945 90.2813 REMARK 3 T TENSOR REMARK 3 T11: 0.2039 T22: 0.3230 REMARK 3 T33: 0.3017 T12: -0.0181 REMARK 3 T13: -0.0824 T23: 0.0327 REMARK 3 L TENSOR REMARK 3 L11: 2.9142 L22: 5.7084 REMARK 3 L33: 2.6404 L12: 1.5518 REMARK 3 L13: -0.7747 L23: 0.3707 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: 0.0374 S13: 0.1086 REMARK 3 S21: -0.1432 S22: -0.1227 S23: 0.0856 REMARK 3 S31: -0.2043 S32: 0.1870 S33: 0.1612 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 5YNL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300004898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13850 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.349 REMARK 200 RESOLUTION RANGE LOW (A) : 63.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MRBUMP REMARK 200 STARTING MODEL: 4HZE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM MALONATE PH 5, 12 % W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, 0.1 M TCEP HYDROCHLORIDE, 10MG/ML REMARK 280 PURIFIED PROTEIN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.59650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.32515 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.92633 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 45.59650 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 26.32515 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.92633 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 45.59650 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 26.32515 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 35.92633 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.65030 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 71.85267 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 52.65030 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 71.85267 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 52.65030 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 71.85267 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: 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 452 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 453 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 454 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 455 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 -42 REMARK 465 HIS A -41 REMARK 465 HIS A -40 REMARK 465 HIS A -39 REMARK 465 HIS A -38 REMARK 465 HIS A -37 REMARK 465 HIS A -36 REMARK 465 SER A -35 REMARK 465 SER A -34 REMARK 465 GLY A -33 REMARK 465 LEU A -32 REMARK 465 VAL A -31 REMARK 465 PRO A -30 REMARK 465 ARG A -29 REMARK 465 GLY A -28 REMARK 465 SER A -27 REMARK 465 GLY A -26 REMARK 465 MET A -25 REMARK 465 LYS A -24 REMARK 465 GLU A -23 REMARK 465 THR A -22 REMARK 465 ALA A -21 REMARK 465 ALA A -20 REMARK 465 ALA A -19 REMARK 465 LYS A -18 REMARK 465 PHE A -17 REMARK 465 GLU A -16 REMARK 465 ARG A -15 REMARK 465 GLN A -14 REMARK 465 HIS A -13 REMARK 465 MET A -12 REMARK 465 ASP A -11 REMARK 465 SER A -10 REMARK 465 PRO A -9 REMARK 465 ASP A -8 REMARK 465 LEU A -7 REMARK 465 GLY A -6 REMARK 465 THR A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 ASP A -1 REMARK 465 LYS A 0 REMARK 465 GLY A 24 REMARK 465 GLY A 25 REMARK 465 GLN A 26 REMARK 465 PRO A 27 REMARK 465 LYS A 28 REMARK 465 ALA A 29 REMARK 465 GLY A 30 REMARK 465 VAL A 31 REMARK 465 ALA A 63 REMARK 465 VAL A 64 REMARK 465 SER A 65 REMARK 465 ILE A 66 REMARK 465 VAL A 67 REMARK 465 SER A 68 REMARK 465 ASP A 69 REMARK 465 THR A 70 REMARK 465 PRO A 71 REMARK 465 ASP A 72 REMARK 465 PRO A 73 REMARK 465 ASP A 74 REMARK 465 ILE A 75 REMARK 465 GLY A 76 REMARK 465 ARG A 77 REMARK 465 LEU A 78 REMARK 465 THR A 165 REMARK 465 SER A 166 REMARK 465 SER A 167 REMARK 465 GLU A 168 REMARK 465 GLU A 169 REMARK 465 SER A 250 REMARK 465 VAL A 251 REMARK 465 ALA A 252 REMARK 465 PRO A 253 REMARK 465 SER A 254 REMARK 465 THR A 255 REMARK 465 GLY A 256 REMARK 465 THR A 257 REMARK 465 ALA A 258 REMARK 465 SER A 292 REMARK 465 LEU A 293 REMARK 465 GLY A 294 REMARK 465 ALA A 295 REMARK 465 LEU A 296 REMARK 465 ALA A 297 REMARK 465 SER A 298 REMARK 465 VAL A 299 REMARK 465 LEU A 319 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 THR A 11 OG1 CG2 REMARK 470 SER A 23 OG REMARK 470 ARG A 86 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 144 CG ND1 CD2 CE1 NE2 REMARK 470 THR A 145 OG1 CG2 REMARK 470 THR A 146 OG1 CG2 REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 SER A 148 OG REMARK 470 GLU A 172 CG CD OE1 OE2 REMARK 470 LYS A 177 CG CD CE NZ REMARK 470 LYS A 199 CG CD CE NZ REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 VAL A 259 CG1 CG2 REMARK 470 ARG A 260 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 301 CG CD OE1 NE2 REMARK 470 GLU A 316 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 HOH A 401 O HOH A 433 1.97 REMARK 500 O VAL A 282 O HOH A 401 1.98 REMARK 500 OE2 GLU A 273 O HOH A 402 2.07 REMARK 500 OE2 GLU A 48 O HOH A 403 2.16 REMARK 500 OD1 ASP A 248 O HOH A 404 2.18 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 PRO A 291 C - N - CA ANGL. DEV. = 9.4 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 59 13.64 -69.07 REMARK 500 SER A 100 16.99 -67.97 REMARK 500 GLU A 147 -48.34 63.30 REMARK 500 LEU A 162 13.59 -148.45 REMARK 500 ASP A 163 115.86 -32.47 REMARK 500 PRO A 171 -120.68 -95.14 REMARK 500 GLU A 172 21.51 -77.71 REMARK 500 PHE A 173 65.92 -114.67 REMARK 500 ARG A 191 -59.52 -146.05 REMARK 500 ILE A 193 87.20 -57.79 REMARK 500 ASN A 231 53.09 -143.07 REMARK 500 ARG A 260 56.15 79.79 REMARK 500 ASN A 290 100.34 50.24 REMARK 500 GLN A 301 39.63 -81.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 109 GLY A 110 149.48 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 A 454 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 455 DISTANCE = 6.47 ANGSTROMS DBREF 5YNL A -42 319 PDB 5YNL 5YNL -42 319 SEQRES 1 A 362 MET HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO SEQRES 2 A 362 ARG GLY SER GLY MET LYS GLU THR ALA ALA ALA LYS PHE SEQRES 3 A 362 GLU ARG GLN HIS MET ASP SER PRO ASP LEU GLY THR ASP SEQRES 4 A 362 ASP ASP ASP LYS MET SER PRO ALA THR SER PRO PHE LEU SEQRES 5 A 362 ALA THR PRO ARG THR ALA GLY ILE VAL GLY CYS PRO PHE SEQRES 6 A 362 SER GLY GLY GLN PRO LYS ALA GLY VAL HIS SER GLY PRO SEQRES 7 A 362 LEU GLN LEU ILE GLU SER GLY LEU LEU ASN ASP ILE GLU SEQRES 8 A 362 ASN LEU GLY TRP THR VAL ASP PHE ALA GLY ALA ASP ALA SEQRES 9 A 362 LEU ALA VAL SER ILE VAL SER ASP THR PRO ASP PRO ASP SEQRES 10 A 362 ILE GLY ARG LEU LYS GLN PRO ARG LEU VAL SER ARG VAL SEQRES 11 A 362 THR LYS ASP VAL ALA ASP ARG VAL TYR ALA HIS ALA SER SEQRES 12 A 362 LYS GLY GLN LEU THR VAL THR LEU GLY GLY ASP HIS SER SEQRES 13 A 362 LEU ALA MET GLY THR VAL SER GLY THR PHE LYS ALA TYR SEQRES 14 A 362 PRO GLU ALA CYS LEU ILE TRP VAL ASP ALA HIS ALA ASP SEQRES 15 A 362 ILE ASN THR PRO HIS THR THR GLU SER GLY ARG LEU HIS SEQRES 16 A 362 GLY CYS PRO VAL SER PHE LEU LEU GLY LEU ASP GLY THR SEQRES 17 A 362 SER SER GLU GLU ILE PRO GLU PHE SER TRP ILE LYS PRO SEQRES 18 A 362 CYS LEU LYS PRO GLU ARG ILE VAL TYR ILE GLY LEU ARG SEQRES 19 A 362 ASP ILE ASP ALA GLY GLU ARG LYS ILE LEU LYS ASP ASN SEQRES 20 A 362 ASN ILE LYS CYS PHE SER MET PHE HIS VAL ASP LYS TYR SEQRES 21 A 362 GLY ILE GLY LYS VAL VAL GLU MET ALA LEU ASP HIS VAL SEQRES 22 A 362 ASN PRO ASP ARG THR ARG PRO ILE HIS LEU SER PHE ASP SEQRES 23 A 362 VAL ASP ALA LEU ASP PRO SER VAL ALA PRO SER THR GLY SEQRES 24 A 362 THR ALA VAL ARG GLY GLY LEU THR PHE ARG GLU GLY HIS SEQRES 25 A 362 TYR ILE CYS GLU ALA ILE ALA GLU THR ASN LEU LEU VAL SEQRES 26 A 362 SER LEU ASP ILE MET GLU ILE ASN PRO SER LEU GLY ALA SEQRES 27 A 362 LEU ALA SER VAL ALA GLN THR VAL ASP VAL GLY ARG SER SEQRES 28 A 362 LEU VAL ARG CYS ALA LEU GLY GLU THR LEU LEU FORMUL 2 HOH *55(H2 O) HELIX 1 AA1 SER A 33 SER A 41 1 9 HELIX 2 AA2 GLY A 42 LEU A 50 1 9 HELIX 3 AA3 GLN A 80 SER A 100 1 21 HELIX 4 AA4 ASP A 111 SER A 113 5 3 HELIX 5 AA5 LEU A 114 TYR A 126 1 13 HELIX 6 AA6 ARG A 150 GLY A 153 5 4 HELIX 7 AA7 CYS A 154 LEU A 160 1 7 HELIX 8 AA8 GLU A 197 ASN A 204 1 8 HELIX 9 AA9 MET A 211 ASN A 231 1 21 HELIX 10 AB1 ASP A 245 LEU A 247 5 3 HELIX 11 AB2 THR A 264 THR A 278 1 15 HELIX 12 AB3 GLN A 301 LEU A 314 1 14 SHEET 1 AA1 8 THR A 53 PHE A 56 0 SHEET 2 AA1 8 THR A 14 CYS A 20 1 N ALA A 15 O THR A 53 SHEET 3 AA1 8 LEU A 104 GLY A 109 1 O VAL A 106 N GLY A 16 SHEET 4 AA1 8 LEU A 281 MET A 287 1 O ILE A 286 N THR A 107 SHEET 5 AA1 8 ILE A 238 ASP A 243 1 N PHE A 242 O MET A 287 SHEET 6 AA1 8 CYS A 130 VAL A 134 1 N ILE A 132 O HIS A 239 SHEET 7 AA1 8 ILE A 185 LEU A 190 1 O VAL A 186 N TRP A 133 SHEET 8 AA1 8 LYS A 207 SER A 210 1 O PHE A 209 N TYR A 187 CRYST1 91.193 91.193 107.779 90.00 90.00 120.00 H 3 9 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 0.010966 0.006331 0.000000 0.00000 SCALE2 0.000000 0.012662 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009278 0.00000