HEADER HYDROLASE 07-JUL-23 8K07 TITLE PSEUDOURIDINE 5'-MONOPHOSPHATE GLYCOSYLASE FROM ARABIDOPSIS THALIANA - TITLE 2 - CITRATE BOUND K185A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOURIDINE-5'-PHOSPHATE GLYCOSIDASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PSEUDOURIDINE 5'-MONOPHOSPHATE GLYCOSYLASE,RIBOSE 5'- COMPND 5 PHOSPHATE ADDUCT,PSIMP GLYCOSIDASE,PSEUDOURIDINE MONOPHOSPHATE COMPND 6 GLYCOSIDASE; COMPND 7 EC: 4.2.1.70; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: PUMY, AT1G50510, F11F12.14; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METALLOENZYME, GLYCOSYLASE, C-NUCLEOSIDE, PSEUDOURIDINE KEYWDS 2 MONOPHOSPHATE, METAL BINDING PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.LEE,S.H.KIM,S.K.RHEE REVDAT 1 15-MAY-24 8K07 0 JRNL AUTH J.LEE,S.H.KIM,S.RHEE JRNL TITL STRUCTURE AND FUNCTION OF THE PSEUDOURIDINE 5'-MONOPHOSPHATE JRNL TITL 2 GLYCOSYLASE PUMY FROM ARABIDOPSIS THALIANA. JRNL REF RNA BIOL. V. 21 1 2024 JRNL REFN ESSN 1555-8584 JRNL PMID 38117089 JRNL DOI 10.1080/15476286.2023.2293340 REMARK 2 REMARK 2 RESOLUTION. 1.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 316071 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 0.630 REMARK 3 FREE R VALUE TEST SET COUNT : 1987 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 24.7960 - 2.6998 0.91 22140 141 0.1902 0.2000 REMARK 3 2 2.6998 - 2.1433 0.98 23717 151 0.1894 0.1994 REMARK 3 3 2.1433 - 1.8725 0.97 23503 150 0.1858 0.1922 REMARK 3 4 1.8725 - 1.7013 0.96 23295 139 0.1933 0.2222 REMARK 3 5 1.7013 - 1.5794 0.95 23187 144 0.1923 0.1951 REMARK 3 6 1.5794 - 1.4863 0.94 22922 148 0.1960 0.2248 REMARK 3 7 1.4863 - 1.4118 0.94 22792 148 0.2139 0.2483 REMARK 3 8 1.4118 - 1.3504 0.93 22671 147 0.2248 0.2474 REMARK 3 9 1.3504 - 1.2984 0.93 22488 144 0.2352 0.2558 REMARK 3 10 1.2984 - 1.2536 0.92 22406 139 0.2561 0.2922 REMARK 3 11 1.2536 - 1.2144 0.91 22090 148 0.3137 0.3196 REMARK 3 12 1.2144 - 1.1797 0.91 22032 125 0.3324 0.3314 REMARK 3 13 1.1797 - 1.1486 0.90 21872 134 0.3419 0.3481 REMARK 3 14 1.1486 - 1.1210 0.78 18969 129 0.3464 0.3819 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) : 26.880 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 : 0.006 6747 REMARK 3 ANGLE : 1.153 9168 REMARK 3 CHIRALITY : 0.047 1117 REMARK 3 PLANARITY : 0.006 1198 REMARK 3 DIHEDRAL : 13.983 2458 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8K07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039199. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 316141 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 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 (%) : 92.4 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.62400 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE PH6.5, 16% PEG REMARK 280 10000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 ALA A 6 REMARK 465 GLN A 7 REMARK 465 SER A 8 REMARK 465 ARG A 9 REMARK 465 ILE A 10 REMARK 465 SER A 11 REMARK 465 ASN A 12 REMARK 465 LEU A 13 REMARK 465 GLN A 14 REMARK 465 ASN A 15 REMARK 465 HIS A 16 REMARK 465 LEU A 17 REMARK 465 SER A 18 REMARK 465 PRO A 19 REMARK 465 LEU A 20 REMARK 465 GLU A 21 REMARK 465 ALA A 22 REMARK 465 ASN A 23 REMARK 465 ASN A 24 REMARK 465 LYS A 25 REMARK 465 LEU A 26 REMARK 465 ARG A 27 REMARK 465 SER A 261 REMARK 465 ALA A 262 REMARK 465 LEU A 331 REMARK 465 GLU A 332 REMARK 465 HIS A 333 REMARK 465 HIS A 334 REMARK 465 HIS A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 LEU B 5 REMARK 465 ALA B 6 REMARK 465 GLN B 7 REMARK 465 SER B 8 REMARK 465 ARG B 9 REMARK 465 ILE B 10 REMARK 465 SER B 11 REMARK 465 ASN B 12 REMARK 465 LEU B 13 REMARK 465 GLN B 14 REMARK 465 ASN B 15 REMARK 465 HIS B 16 REMARK 465 LEU B 17 REMARK 465 SER B 18 REMARK 465 PRO B 19 REMARK 465 LEU B 20 REMARK 465 GLU B 21 REMARK 465 ALA B 22 REMARK 465 ASN B 23 REMARK 465 ASN B 24 REMARK 465 LYS B 25 REMARK 465 LEU B 26 REMARK 465 ARG B 27 REMARK 465 LEU B 332 REMARK 465 GLU B 333 REMARK 465 HIS B 334 REMARK 465 HIS B 335 REMARK 465 HIS B 336 REMARK 465 HIS B 337 REMARK 465 HIS B 338 REMARK 465 HIS B 339 REMARK 465 HIS B 340 REMARK 465 HIS B 341 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 SER C 3 REMARK 465 SER C 4 REMARK 465 LEU C 5 REMARK 465 ALA C 6 REMARK 465 GLN C 7 REMARK 465 SER C 8 REMARK 465 ARG C 9 REMARK 465 ILE C 10 REMARK 465 SER C 11 REMARK 465 ASN C 12 REMARK 465 LEU C 13 REMARK 465 GLN C 14 REMARK 465 ASN C 15 REMARK 465 HIS C 16 REMARK 465 LEU C 17 REMARK 465 SER C 18 REMARK 465 PRO C 19 REMARK 465 LEU C 20 REMARK 465 GLU C 21 REMARK 465 ALA C 22 REMARK 465 ASN C 23 REMARK 465 ASN C 24 REMARK 465 LYS C 25 REMARK 465 LEU C 26 REMARK 465 ARG C 27 REMARK 465 SER C 28 REMARK 465 ALA C 262 REMARK 465 ALA C 263 REMARK 465 GLY C 264 REMARK 465 ASN C 265 REMARK 465 LEU C 266 REMARK 465 ILE C 267 REMARK 465 GLU C 268 REMARK 465 LEU C 331 REMARK 465 GLU C 332 REMARK 465 HIS C 333 REMARK 465 HIS C 334 REMARK 465 HIS C 335 REMARK 465 HIS C 336 REMARK 465 HIS C 337 REMARK 465 HIS C 338 REMARK 465 HIS C 339 REMARK 465 HIS C 340 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 OD1 ASN C 314 O HOH C 501 2.01 REMARK 500 O LEU A 103 O HOH A 501 2.04 REMARK 500 O PRO C 255 O HOH C 501 2.05 REMARK 500 O HOH B 752 O HOH B 781 2.18 REMARK 500 NZ LYS A 208 O HOH A 502 2.19 REMARK 500 O HOH A 604 O HOH A 696 2.19 REMARK 500 O HOH A 703 O HOH C 731 2.19 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 C 246 NE - CZ - NH1 ANGL. DEV. = 3.5 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 PHE A 215 -97.07 68.64 REMARK 500 PHE B 216 -96.78 69.21 REMARK 500 PHE C 215 -95.14 67.35 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 781 DISTANCE = 7.33 ANGSTROMS REMARK 525 HOH B 789 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH C 739 DISTANCE = 7.99 ANGSTROMS 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 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 164 OD1 REMARK 620 2 CIT A 402 O7 176.2 REMARK 620 3 CIT A 402 O5 107.0 72.4 REMARK 620 4 HOH A 528 O 86.7 89.6 97.3 REMARK 620 5 HOH A 595 O 95.5 88.3 91.2 170.2 REMARK 620 6 HOH C 555 O 87.7 92.8 165.2 82.4 88.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 563 O REMARK 620 2 ASP B 165 OD1 87.8 REMARK 620 3 CIT B 402 O6 165.2 107.0 REMARK 620 4 CIT B 402 O7 91.9 177.1 73.3 REMARK 620 5 HOH B 520 O 84.7 85.3 96.8 91.8 REMARK 620 6 HOH B 591 O 87.7 95.3 90.4 87.6 172.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 548 O REMARK 620 2 ASP C 164 OD1 90.4 REMARK 620 3 CIT C 402 O7 91.4 176.1 REMARK 620 4 CIT C 402 O6 164.6 105.0 73.3 REMARK 620 5 HOH C 518 O 83.9 85.3 91.5 98.3 REMARK 620 6 HOH C 554 O 88.1 96.6 86.9 88.9 171.8 REMARK 620 N 1 2 3 4 5 DBREF 8K07 A 1 330 UNP Q84K35 PUMY_ARATH 1 330 DBREF 8K07 B 1 331 UNP Q84K35 PUMY_ARATH 1 330 DBREF 8K07 C 1 330 UNP Q84K35 PUMY_ARATH 1 330 SEQADV 8K07 ALA A 185 UNP Q84K35 LYS 185 ENGINEERED MUTATION SEQADV 8K07 LEU A 331 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 GLU A 332 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS A 333 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS A 334 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS A 335 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS A 336 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS A 337 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS A 338 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS A 339 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS A 340 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 ALA B 186 UNP Q84K35 LYS 185 ENGINEERED MUTATION SEQADV 8K07 LEU B 332 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 GLU B 333 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS B 334 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS B 335 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS B 336 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS B 337 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS B 338 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS B 339 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS B 340 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS B 341 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 ALA C 185 UNP Q84K35 LYS 185 ENGINEERED MUTATION SEQADV 8K07 LEU C 331 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 GLU C 332 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS C 333 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS C 334 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS C 335 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS C 336 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS C 337 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS C 338 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS C 339 UNP Q84K35 EXPRESSION TAG SEQADV 8K07 HIS C 340 UNP Q84K35 EXPRESSION TAG SEQRES 1 A 340 MET ALA SER SER LEU ALA GLN SER ARG ILE SER ASN LEU SEQRES 2 A 340 GLN ASN HIS LEU SER PRO LEU GLU ALA ASN ASN LYS LEU SEQRES 3 A 340 ARG SER LEU VAL LYS ILE SER PRO GLN VAL SER GLU ALA SEQRES 4 A 340 LEU SER ASN GLY ARG ALA VAL VAL ALA LEU GLU SER THR SEQRES 5 A 340 ILE ILE SER HIS GLY MET PRO TYR PRO GLN ASN LEU GLN SEQRES 6 A 340 THR ALA LYS GLU VAL GLU SER ILE VAL ARG GLU ASN GLY SEQRES 7 A 340 ALA ILE PRO ALA THR ILE ALA ILE LEU ASN GLY VAL PRO SEQRES 8 A 340 CYS ILE GLY LEU SER GLU GLU GLU LEU GLU ARG LEU ALA SEQRES 9 A 340 SER LEU GLY LYS SER VAL GLN LYS THR ALA GLY ARG ASP SEQRES 10 A 340 ILE ALA ASN VAL VAL ALA THR ARG GLY ASN GLY ALA THR SEQRES 11 A 340 THR VAL SER ALA THR LEU PHE PHE ALA SER MET VAL GLY SEQRES 12 A 340 ILE GLN VAL PHE VAL THR GLY GLY ILE GLY GLY VAL HIS SEQRES 13 A 340 ARG HIS ALA ASN HIS SER MET ASP ILE SER SER ASP LEU SEQRES 14 A 340 THR ALA LEU GLY ARG THR PRO ILE ALA VAL ILE SER ALA SEQRES 15 A 340 GLY VAL ALA SER ILE LEU ASP ILE PRO LYS THR LEU GLU SEQRES 16 A 340 TYR LEU GLU THR GLN GLU VAL TYR VAL ALA ALA TYR LYS SEQRES 17 A 340 SER ASP GLU PHE PRO ALA PHE PHE THR GLU LYS SER GLY SEQRES 18 A 340 CYS LYS ALA PRO SER ARG VAL ASN SER PRO GLU ASP CYS SEQRES 19 A 340 ALA ARG VAL ILE ASP ALA ASN MET LYS LEU ASN ARG GLN SEQRES 20 A 340 ALA GLY ILE LEU PHE ALA ILE PRO ILE PRO LYS HIS HIS SEQRES 21 A 340 SER ALA ALA GLY ASN LEU ILE GLU SER ALA THR GLN ARG SEQRES 22 A 340 ALA LEU THR GLU ALA ARG GLU GLN ASN VAL THR GLY ASN SEQRES 23 A 340 ALA GLU THR PRO PHE LEU LEU ALA ARG VAL ASN GLU LEU SEQRES 24 A 340 THR GLY GLY THR SER LEU ALA ALA ASN ILE ALA LEU VAL SEQRES 25 A 340 LYS ASN ASN ALA LEU ILE GLY SER GLN ILE ALA VAL ALA SEQRES 26 A 340 LEU SER GLN LEU MET LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 27 A 340 HIS HIS SEQRES 1 B 340 MET ALA SER SER LEU ALA GLN SER ARG ILE SER ASN LEU SEQRES 2 B 340 GLN ASN HIS LEU SER PRO LEU GLU ALA ASN ASN LYS LEU SEQRES 3 B 340 ARG SER LEU VAL LYS ILE SER PRO GLN VAL SER GLU ALA SEQRES 4 B 340 LEU SER ASN GLY ARG ALA VAL VAL ALA LEU GLU SER THR SEQRES 5 B 340 ILE ILE SER HIS GLY MET PRO TYR PRO GLN ASN LEU GLN SEQRES 6 B 340 THR ALA LYS GLU VAL GLU SER ILE VAL ARG GLU ASN GLY SEQRES 7 B 340 ALA ILE PRO ALA THR ILE ALA ILE LEU ASN GLY VAL PRO SEQRES 8 B 340 CYS ILE GLY LEU SER GLU GLU GLU LEU GLU ARG LEU ALA SEQRES 9 B 340 SER LEU GLY LYS SER VAL GLN LYS THR ALA GLY ARG ASP SEQRES 10 B 340 ILE ALA ASN VAL VAL ALA THR ARG GLY ASN GLY ALA THR SEQRES 11 B 340 THR VAL SER ALA THR LEU PHE PHE ALA SER MET VAL GLY SEQRES 12 B 340 ILE GLN VAL PHE VAL THR GLY GLY ILE GLY GLY VAL HIS SEQRES 13 B 340 ARG HIS ALA ASN HIS SER MET ASP ILE SER SER ASP LEU SEQRES 14 B 340 THR ALA LEU GLY ARG THR PRO ILE ALA VAL ILE SER ALA SEQRES 15 B 340 GLY VAL ALA SER ILE LEU ASP ILE PRO LYS THR LEU GLU SEQRES 16 B 340 TYR LEU GLU THR GLN GLU VAL TYR VAL ALA ALA TYR LYS SEQRES 17 B 340 SER ASP GLU PHE PRO ALA PHE PHE THR GLU LYS SER GLY SEQRES 18 B 340 CYS LYS ALA PRO SER ARG VAL ASN SER PRO GLU ASP CYS SEQRES 19 B 340 ALA ARG VAL ILE ASP ALA ASN MET LYS LEU ASN ARG GLN SEQRES 20 B 340 ALA GLY ILE LEU PHE ALA ILE PRO ILE PRO LYS HIS HIS SEQRES 21 B 340 SER ALA ALA GLY ASN LEU ILE GLU SER ALA THR GLN ARG SEQRES 22 B 340 ALA LEU THR GLU ALA ARG GLU GLN ASN VAL THR GLY ASN SEQRES 23 B 340 ALA GLU THR PRO PHE LEU LEU ALA ARG VAL ASN GLU LEU SEQRES 24 B 340 THR GLY GLY THR SER LEU ALA ALA ASN ILE ALA LEU VAL SEQRES 25 B 340 LYS ASN ASN ALA LEU ILE GLY SER GLN ILE ALA VAL ALA SEQRES 26 B 340 LEU SER GLN LEU MET LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 27 B 340 HIS HIS SEQRES 1 C 340 MET ALA SER SER LEU ALA GLN SER ARG ILE SER ASN LEU SEQRES 2 C 340 GLN ASN HIS LEU SER PRO LEU GLU ALA ASN ASN LYS LEU SEQRES 3 C 340 ARG SER LEU VAL LYS ILE SER PRO GLN VAL SER GLU ALA SEQRES 4 C 340 LEU SER ASN GLY ARG ALA VAL VAL ALA LEU GLU SER THR SEQRES 5 C 340 ILE ILE SER HIS GLY MET PRO TYR PRO GLN ASN LEU GLN SEQRES 6 C 340 THR ALA LYS GLU VAL GLU SER ILE VAL ARG GLU ASN GLY SEQRES 7 C 340 ALA ILE PRO ALA THR ILE ALA ILE LEU ASN GLY VAL PRO SEQRES 8 C 340 CYS ILE GLY LEU SER GLU GLU GLU LEU GLU ARG LEU ALA SEQRES 9 C 340 SER LEU GLY LYS SER VAL GLN LYS THR ALA GLY ARG ASP SEQRES 10 C 340 ILE ALA ASN VAL VAL ALA THR ARG GLY ASN GLY ALA THR SEQRES 11 C 340 THR VAL SER ALA THR LEU PHE PHE ALA SER MET VAL GLY SEQRES 12 C 340 ILE GLN VAL PHE VAL THR GLY GLY ILE GLY GLY VAL HIS SEQRES 13 C 340 ARG HIS ALA ASN HIS SER MET ASP ILE SER SER ASP LEU SEQRES 14 C 340 THR ALA LEU GLY ARG THR PRO ILE ALA VAL ILE SER ALA SEQRES 15 C 340 GLY VAL ALA SER ILE LEU ASP ILE PRO LYS THR LEU GLU SEQRES 16 C 340 TYR LEU GLU THR GLN GLU VAL TYR VAL ALA ALA TYR LYS SEQRES 17 C 340 SER ASP GLU PHE PRO ALA PHE PHE THR GLU LYS SER GLY SEQRES 18 C 340 CYS LYS ALA PRO SER ARG VAL ASN SER PRO GLU ASP CYS SEQRES 19 C 340 ALA ARG VAL ILE ASP ALA ASN MET LYS LEU ASN ARG GLN SEQRES 20 C 340 ALA GLY ILE LEU PHE ALA ILE PRO ILE PRO LYS HIS HIS SEQRES 21 C 340 SER ALA ALA GLY ASN LEU ILE GLU SER ALA THR GLN ARG SEQRES 22 C 340 ALA LEU THR GLU ALA ARG GLU GLN ASN VAL THR GLY ASN SEQRES 23 C 340 ALA GLU THR PRO PHE LEU LEU ALA ARG VAL ASN GLU LEU SEQRES 24 C 340 THR GLY GLY THR SER LEU ALA ALA ASN ILE ALA LEU VAL SEQRES 25 C 340 LYS ASN ASN ALA LEU ILE GLY SER GLN ILE ALA VAL ALA SEQRES 26 C 340 LEU SER GLN LEU MET LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 27 C 340 HIS HIS HET MN A 401 1 HET CIT A 402 13 HET MN B 401 1 HET CIT B 402 13 HET MN C 401 1 HET CIT C 402 13 HETNAM MN MANGANESE (II) ION HETNAM CIT CITRIC ACID FORMUL 4 MN 3(MN 2+) FORMUL 5 CIT 3(C6 H8 O7) FORMUL 10 HOH *809(H2 O) HELIX 1 AA1 SER A 33 GLY A 43 1 11 HELIX 2 AA2 SER A 51 HIS A 56 1 6 HELIX 3 AA3 PRO A 61 ASN A 77 1 17 HELIX 4 AA4 SER A 96 GLY A 107 1 12 HELIX 5 AA5 LYS A 108 VAL A 110 5 3 HELIX 6 AA6 ALA A 114 ARG A 116 5 3 HELIX 7 AA7 ASP A 117 THR A 124 1 8 HELIX 8 AA8 THR A 131 VAL A 142 1 12 HELIX 9 AA9 HIS A 158 MET A 163 1 6 HELIX 10 AB1 SER A 166 ARG A 174 1 9 HELIX 11 AB2 ASP A 189 GLN A 200 1 12 HELIX 12 AB3 SER A 230 LEU A 244 1 15 HELIX 13 AB4 GLY A 264 GLN A 281 1 18 HELIX 14 AB5 THR A 284 ASN A 286 5 3 HELIX 15 AB6 ALA A 287 THR A 300 1 14 HELIX 16 AB7 GLY A 302 MET A 330 1 29 HELIX 17 AB8 SER B 34 ASN B 43 1 10 HELIX 18 AB9 SER B 52 HIS B 57 1 6 HELIX 19 AC1 PRO B 62 ASN B 78 1 17 HELIX 20 AC2 SER B 97 GLY B 108 1 12 HELIX 21 AC3 LYS B 109 VAL B 111 5 3 HELIX 22 AC4 ALA B 115 ARG B 117 5 3 HELIX 23 AC5 ASP B 118 THR B 125 1 8 HELIX 24 AC6 THR B 132 GLY B 144 1 13 HELIX 25 AC7 HIS B 159 MET B 164 1 6 HELIX 26 AC8 SER B 167 ARG B 175 1 9 HELIX 27 AC9 ASP B 190 GLN B 201 1 12 HELIX 28 AD1 SER B 231 ASN B 246 1 16 HELIX 29 AD2 PRO B 258 ALA B 263 5 6 HELIX 30 AD3 ALA B 264 GLN B 282 1 19 HELIX 31 AD4 THR B 285 ASN B 287 5 3 HELIX 32 AD5 ALA B 288 THR B 301 1 14 HELIX 33 AD6 GLY B 303 MET B 331 1 29 HELIX 34 AD7 SER C 33 ASN C 42 1 10 HELIX 35 AD8 SER C 51 GLY C 57 1 7 HELIX 36 AD9 PRO C 61 ASN C 77 1 17 HELIX 37 AE1 SER C 96 LEU C 106 1 11 HELIX 38 AE2 GLY C 107 VAL C 110 5 4 HELIX 39 AE3 ALA C 114 ARG C 116 5 3 HELIX 40 AE4 ASP C 117 THR C 124 1 8 HELIX 41 AE5 THR C 131 GLY C 143 1 13 HELIX 42 AE6 HIS C 158 MET C 163 1 6 HELIX 43 AE7 SER C 166 ARG C 174 1 9 HELIX 44 AE8 ASP C 189 GLN C 200 1 12 HELIX 45 AE9 SER C 230 LEU C 244 1 15 HELIX 46 AF1 ALA C 270 GLN C 281 1 12 HELIX 47 AF2 THR C 284 ASN C 286 5 3 HELIX 48 AF3 ALA C 287 THR C 300 1 14 HELIX 49 AF4 GLY C 302 MET C 330 1 29 SHEET 1 AA1 9 LYS A 31 ILE A 32 0 SHEET 2 AA1 9 VAL A 90 ILE A 93 1 O PRO A 91 N LYS A 31 SHEET 3 AA1 9 ILE A 80 LEU A 87 -1 N ALA A 85 O CYS A 92 SHEET 4 AA1 9 VAL A 46 LEU A 49 1 N VAL A 47 O ALA A 82 SHEET 5 AA1 9 VAL A 146 VAL A 148 1 O VAL A 146 N ALA A 48 SHEET 6 AA1 9 ALA A 178 SER A 181 1 O ILE A 180 N PHE A 147 SHEET 7 AA1 9 ILE A 250 ALA A 253 1 O ILE A 250 N VAL A 179 SHEET 8 AA1 9 TYR A 203 TYR A 207 1 N TYR A 203 O LEU A 251 SHEET 9 AA1 9 ARG A 227 VAL A 228 1 O VAL A 228 N ALA A 206 SHEET 1 AA2 2 GLN A 111 THR A 113 0 SHEET 2 AA2 2 GLY A 128 THR A 130 1 O ALA A 129 N THR A 113 SHEET 1 AA3 9 LYS B 32 ILE B 33 0 SHEET 2 AA3 9 VAL B 91 ILE B 94 1 O PRO B 92 N LYS B 32 SHEET 3 AA3 9 ILE B 81 LEU B 88 -1 N ALA B 86 O CYS B 93 SHEET 4 AA3 9 VAL B 47 LEU B 50 1 N VAL B 48 O ALA B 83 SHEET 5 AA3 9 VAL B 147 VAL B 149 1 O VAL B 147 N ALA B 49 SHEET 6 AA3 9 ALA B 179 SER B 182 1 O ILE B 181 N PHE B 148 SHEET 7 AA3 9 ILE B 251 ALA B 254 1 O ILE B 251 N VAL B 180 SHEET 8 AA3 9 TYR B 204 TYR B 208 1 N TYR B 204 O LEU B 252 SHEET 9 AA3 9 ARG B 228 VAL B 229 1 O VAL B 229 N ALA B 207 SHEET 1 AA4 2 GLN B 112 THR B 114 0 SHEET 2 AA4 2 GLY B 129 THR B 131 1 O ALA B 130 N THR B 114 SHEET 1 AA5 9 LYS C 31 ILE C 32 0 SHEET 2 AA5 9 VAL C 90 ILE C 93 1 O PRO C 91 N LYS C 31 SHEET 3 AA5 9 ILE C 80 LEU C 87 -1 N ALA C 85 O CYS C 92 SHEET 4 AA5 9 VAL C 46 LEU C 49 1 N VAL C 47 O ALA C 82 SHEET 5 AA5 9 VAL C 146 VAL C 148 1 O VAL C 146 N ALA C 48 SHEET 6 AA5 9 ALA C 178 SER C 181 1 O ILE C 180 N PHE C 147 SHEET 7 AA5 9 ILE C 250 ALA C 253 1 O ILE C 250 N VAL C 179 SHEET 8 AA5 9 TYR C 203 TYR C 207 1 N TYR C 203 O LEU C 251 SHEET 9 AA5 9 ARG C 227 VAL C 228 1 O VAL C 228 N ALA C 206 SHEET 1 AA6 2 GLN C 111 THR C 113 0 SHEET 2 AA6 2 GLY C 128 THR C 130 1 O ALA C 129 N THR C 113 LINK OD1 ASP A 164 MN MN A 401 1555 1555 2.14 LINK MN MN A 401 O7 CIT A 402 1555 1555 2.28 LINK MN MN A 401 O5 CIT A 402 1555 1555 2.20 LINK MN MN A 401 O HOH A 528 1555 1555 2.17 LINK MN MN A 401 O HOH A 595 1555 1555 2.10 LINK MN MN A 401 O HOH C 555 1555 1555 2.24 LINK O HOH A 563 MN MN B 401 1555 1555 2.22 LINK OD1 ASP B 165 MN MN B 401 1555 1555 2.15 LINK MN MN B 401 O6 CIT B 402 1555 1555 2.20 LINK MN MN B 401 O7 CIT B 402 1555 1555 2.24 LINK MN MN B 401 O HOH B 520 1555 1555 2.16 LINK MN MN B 401 O HOH B 591 1555 1555 2.13 LINK O HOH B 548 MN MN C 401 1555 1555 2.25 LINK OD1 ASP C 164 MN MN C 401 1555 1555 2.14 LINK MN MN C 401 O7 CIT C 402 1555 1555 2.28 LINK MN MN C 401 O6 CIT C 402 1555 1555 2.22 LINK MN MN C 401 O HOH C 518 1555 1555 2.12 LINK MN MN C 401 O HOH C 554 1555 1555 2.13 CISPEP 1 TYR A 60 PRO A 61 0 5.22 CISPEP 2 TYR B 61 PRO B 62 0 2.60 CISPEP 3 TYR C 60 PRO C 61 0 6.62 CRYST1 57.299 68.518 73.095 117.88 94.31 109.38 P 1 3 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 0.017452 0.006139 0.005318 0.00000 SCALE2 0.000000 0.015471 0.009508 0.00000 SCALE3 0.000000 0.000000 0.016104 0.00000