HEADER TRANSFERASE 14-OCT-17 5YKJ TITLE STRUCTURAL BASIS OF THE THIOL RESOLVING MECHANISM IN YEAST TITLE 2 MITOCHONDRIAL 1-CYS PEROXIREDOXIN VIA GLUTATHIONE/THIOREDOXIN SYSTEMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIREDOXIN PRX1, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 49-261; COMPND 5 SYNONYM: PRX,1-CYS PRX,MITOCHONDRIAL THIOL PEROXIDASE,MTPX, COMPND 6 THIOREDOXIN PEROXIDASE; COMPND 7 EC: 1.11.1.15; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: PRX1, YBL064C, YBL0503, YBL0524; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SACCHAROMYCES CEREVISIAE, 1-CYS PEROXIREDOXIN, THIOREDOXIN, KEYWDS 2 GLUTATHIONE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.C.LI,J.YANG,M.J.YANG,L.LIU,C.T.PENG,T.LI,L.H.HE,Y.J.SONG,Y.B.ZHU, AUTHOR 2 N.L.ZHAO,C.ZHAO,R.BAO REVDAT 2 06-NOV-19 5YKJ 1 JRNL REVDAT 1 24-OCT-18 5YKJ 0 JRNL AUTH C.C.LI,J.YANG,M.J.YANG,L.LIU,C.T.PENG,T.LI,L.H.HE,Y.J.SONG, JRNL AUTH 2 Y.B.ZHU,N.L.ZHAO,C.ZHAO,R.BAO JRNL TITL STRUCTURAL BASIS OF THE THIOL RESOLVING MECHANISM IN YEAST JRNL TITL 2 MITOCHONDRIAL 1-CYS PEROXIREDOXIN VIA JRNL TITL 3 GLUTATHIONE/THIOREDOXIN SYSTEMS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 34452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.810 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 43.1730 - 3.6876 1.00 2505 154 0.1685 0.1623 REMARK 3 2 3.6876 - 2.9271 1.00 2382 148 0.1448 0.1549 REMARK 3 3 2.9271 - 2.5572 1.00 2341 143 0.1480 0.1820 REMARK 3 4 2.5572 - 2.3234 1.00 2325 144 0.1414 0.1479 REMARK 3 5 2.3234 - 2.1569 1.00 2320 143 0.1402 0.1518 REMARK 3 6 2.1569 - 2.0297 1.00 2314 143 0.1535 0.1915 REMARK 3 7 2.0297 - 1.9280 1.00 2301 141 0.1577 0.1722 REMARK 3 8 1.9280 - 1.8441 1.00 2282 141 0.1802 0.2251 REMARK 3 9 1.8441 - 1.7731 1.00 2292 141 0.2129 0.2504 REMARK 3 10 1.7731 - 1.7119 1.00 2292 142 0.2369 0.2683 REMARK 3 11 1.7119 - 1.6584 1.00 2285 141 0.2558 0.3091 REMARK 3 12 1.6584 - 1.6110 1.00 2265 138 0.2814 0.2694 REMARK 3 13 1.6110 - 1.5686 1.00 2274 141 0.2960 0.2959 REMARK 3 14 1.5686 - 1.5303 1.00 2274 140 0.3190 0.3295 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.850 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 : 0.031 1756 REMARK 3 ANGLE : 1.982 2384 REMARK 3 CHIRALITY : 0.154 269 REMARK 3 PLANARITY : 0.009 307 REMARK 3 DIHEDRAL : 19.093 650 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 48 THROUGH 119 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5075 8.3635 9.6176 REMARK 3 T TENSOR REMARK 3 T11: 0.0991 T22: 0.0746 REMARK 3 T33: 0.0970 T12: 0.0114 REMARK 3 T13: -0.0058 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 0.6290 L22: 0.6487 REMARK 3 L33: 0.7104 L12: -0.0050 REMARK 3 L13: -0.2466 L23: -0.0506 REMARK 3 S TENSOR REMARK 3 S11: -0.0306 S12: -0.0696 S13: -0.0866 REMARK 3 S21: 0.0031 S22: -0.0117 S23: -0.0835 REMARK 3 S31: 0.1287 S32: 0.0440 S33: 0.0330 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 120 THROUGH 149 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.5696 7.4566 21.2037 REMARK 3 T TENSOR REMARK 3 T11: 0.1057 T22: 0.1350 REMARK 3 T33: 0.1122 T12: 0.0256 REMARK 3 T13: 0.0000 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 1.2001 L22: 2.5044 REMARK 3 L33: 1.0279 L12: 0.9753 REMARK 3 L13: -0.4071 L23: -0.5241 REMARK 3 S TENSOR REMARK 3 S11: 0.0337 S12: -0.2142 S13: -0.0836 REMARK 3 S21: 0.1520 S22: -0.1203 S23: 0.0809 REMARK 3 S31: 0.0767 S32: 0.0810 S33: 0.0569 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 150 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.0389 24.0468 13.7271 REMARK 3 T TENSOR REMARK 3 T11: 0.1077 T22: 0.1355 REMARK 3 T33: 0.1272 T12: -0.0184 REMARK 3 T13: -0.0033 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.6810 L22: 2.0587 REMARK 3 L33: 1.3934 L12: -0.1694 REMARK 3 L13: 0.3662 L23: 0.0197 REMARK 3 S TENSOR REMARK 3 S11: -0.0572 S12: -0.3307 S13: 0.1634 REMARK 3 S21: 0.2345 S22: -0.0635 S23: 0.1594 REMARK 3 S31: -0.2818 S32: 0.0063 S33: 0.0918 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.7339 7.5114 -6.1109 REMARK 3 T TENSOR REMARK 3 T11: 0.1142 T22: 0.0666 REMARK 3 T33: 0.0845 T12: 0.0019 REMARK 3 T13: 0.0158 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.5252 L22: 0.4258 REMARK 3 L33: 1.0048 L12: -0.2078 REMARK 3 L13: 0.2829 L23: -0.0455 REMARK 3 S TENSOR REMARK 3 S11: 0.0434 S12: 0.0667 S13: -0.0495 REMARK 3 S21: -0.0706 S22: -0.0334 S23: -0.0157 REMARK 3 S31: 0.1905 S32: 0.0405 S33: -0.0009 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 246 THROUGH 260 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.1611 3.1524 -24.2970 REMARK 3 T TENSOR REMARK 3 T11: 0.1785 T22: 0.0929 REMARK 3 T33: 0.1131 T12: 0.0325 REMARK 3 T13: -0.0116 T23: -0.0420 REMARK 3 L TENSOR REMARK 3 L11: 2.8447 L22: 3.2439 REMARK 3 L33: 1.5386 L12: -0.6974 REMARK 3 L13: -0.3178 L23: -0.3027 REMARK 3 S TENSOR REMARK 3 S11: 0.0647 S12: 0.1493 S13: -0.1726 REMARK 3 S21: 0.0917 S22: -0.0102 S23: 0.0490 REMARK 3 S31: 0.3793 S32: -0.0064 S33: -0.0953 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 5YKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005445. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-16 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97022 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34456 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 43.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 22.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.16100 REMARK 200 FOR THE DATA SET : 14.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 18.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.73900 REMARK 200 FOR SHELL : 3.870 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% (W/V) PEG-2000 MME ,100MM TRIS REMARK 280 BASE/HYDROCHLORIC ACID PH 4.7., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 31.39200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.01500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.01500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.69600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.01500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.01500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.08800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.01500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.01500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.69600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.01500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.01500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.08800 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 31.39200 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 591 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 LYS A 261 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 166 O HOH A 401 1.77 REMARK 500 OE1 GLU A 216 O HOH A 402 2.04 REMARK 500 O HOH A 409 O HOH A 535 2.06 REMARK 500 O HOH A 500 O HOH A 627 2.07 REMARK 500 O HOH A 515 O HOH A 592 2.12 REMARK 500 CG2 THR A 213 O HOH A 452 2.12 REMARK 500 OG1 THR A 88 O HOH A 403 2.12 REMARK 500 O HOH A 404 O HOH A 530 2.13 REMARK 500 O HOH A 436 O HOH A 610 2.14 REMARK 500 O HOH A 410 O HOH A 570 2.15 REMARK 500 O HOH A 509 O HOH A 572 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 461 O HOH A 461 7555 2.14 REMARK 500 O HOH A 558 O HOH A 558 7555 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 161 CD GLU A 161 OE2 -0.068 REMARK 500 SER A 194 CB SER A 194 OG -0.081 REMARK 500 GLU A 202 CD GLU A 202 OE1 -0.072 REMARK 500 GLU A 250 CD GLU A 250 OE2 -0.072 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 149 NE - CZ - NH2 ANGL. DEV. = -4.0 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 ASN A 52 -2.70 81.28 REMARK 500 ARG A 175 12.63 -142.15 REMARK 500 ALA A 227 -6.69 86.87 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 629 DISTANCE = 6.05 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 302 DBREF 5YKJ A 49 261 UNP P34227 PRX1_YEAST 49 261 SEQADV 5YKJ MET A 48 UNP P34227 EXPRESSION TAG SEQRES 1 A 214 MET LEU ARG ILE ASN SER ASP ALA PRO ASN PHE ASP ALA SEQRES 2 A 214 ASP THR THR VAL GLY LYS ILE ASN PHE TYR ASP TYR LEU SEQRES 3 A 214 GLY ASP SER TRP GLY VAL LEU PHE SER HIS PRO ALA ASP SEQRES 4 A 214 PHE THR PRO VAL CSO THR THR GLU VAL SER ALA PHE ALA SEQRES 5 A 214 LYS LEU LYS PRO GLU PHE ASP LYS ARG ASN VAL LYS LEU SEQRES 6 A 214 ILE GLY LEU SER VAL GLU ASP VAL GLU SER HIS GLU LYS SEQRES 7 A 214 TRP ILE GLN ASP ILE LYS GLU ILE ALA LYS VAL LYS ASN SEQRES 8 A 214 VAL GLY PHE PRO ILE ILE GLY ASP THR PHE ARG ASN VAL SEQRES 9 A 214 ALA PHE LEU TYR ASP MET VAL ASP ALA GLU GLY PHE LYS SEQRES 10 A 214 ASN ILE ASN ASP GLY SER LEU LYS THR VAL ARG SER VAL SEQRES 11 A 214 PHE VAL ILE ASP PRO LYS LYS LYS ILE ARG LEU ILE PHE SEQRES 12 A 214 THR TYR PRO SER THR VAL GLY ARG ASN THR SER GLU VAL SEQRES 13 A 214 LEU ARG VAL ILE ASP ALA LEU GLN LEU THR ASP LYS GLU SEQRES 14 A 214 GLY VAL VAL THR PRO ILE ASN TRP GLN PRO ALA ASP ASP SEQRES 15 A 214 VAL ILE ILE PRO PRO SER VAL SER ASN ASP GLU ALA LYS SEQRES 16 A 214 ALA LYS PHE GLY GLN PHE ASN GLU ILE LYS PRO TYR LEU SEQRES 17 A 214 ARG PHE THR LYS SER LYS MODRES 5YKJ CSO A 91 CYS MODIFIED RESIDUE HET CSO A 91 12 HET GOL A 301 13 HET NA A 302 1 HETNAM CSO S-HYDROXYCYSTEINE HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 GOL C3 H8 O3 FORMUL 3 NA NA 1+ FORMUL 4 HOH *229(H2 O) HELIX 1 AA1 PHE A 69 GLY A 74 1 6 HELIX 2 AA2 THR A 88 LEU A 101 1 14 HELIX 3 AA3 LEU A 101 LYS A 107 1 7 HELIX 4 AA4 ASP A 119 LYS A 135 1 17 HELIX 5 AA5 ARG A 149 TYR A 155 1 7 HELIX 6 AA6 ASN A 199 GLY A 217 1 19 HELIX 7 AA7 SER A 237 GLY A 246 1 10 SHEET 1 AA1 2 ASP A 59 ALA A 60 0 SHEET 2 AA1 2 ILE A 67 ASN A 68 -1 O ILE A 67 N ALA A 60 SHEET 1 AA2 5 ILE A 143 GLY A 145 0 SHEET 2 AA2 5 VAL A 110 SER A 116 1 N GLY A 114 O ILE A 144 SHEET 3 AA2 5 TRP A 77 HIS A 83 1 N TRP A 77 O LYS A 111 SHEET 4 AA2 5 SER A 176 ILE A 180 -1 O ILE A 180 N GLY A 78 SHEET 5 AA2 5 ILE A 186 THR A 191 -1 O ARG A 187 N VAL A 179 SHEET 1 AA3 3 VAL A 230 ILE A 231 0 SHEET 2 AA3 3 LEU A 255 THR A 258 -1 O THR A 258 N VAL A 230 SHEET 3 AA3 3 ASN A 249 LYS A 252 -1 N ASN A 249 O PHE A 257 LINK C VAL A 90 N CSO A 91 1555 1555 1.31 LINK C CSO A 91 N THR A 92 1555 1555 1.32 SITE 1 AC1 5 THR A 88 PRO A 89 VAL A 90 SER A 194 SITE 2 AC1 5 PRO A 234 SITE 1 AC2 1 PHE A 248 CRYST1 84.030 84.030 62.784 90.00 90.00 90.00 P 41 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 0.011901 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011901 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015928 0.00000