HEADER HYDROLASE 04-JUL-15 5CDL TITLE PROLINE DIPEPTIDASE FROM DEINOCOCCUS RADIODURANS (SELENOMETHIONINE TITLE 2 DERIVATIVE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLINE DIPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 243230; SOURCE 4 STRAIN: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / SOURCE 5 NCIMB 9279 / R1 / VKM B-1422; SOURCE 6 ATCC: 13939; SOURCE 7 GENE: DR_1246; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PST50TR KEYWDS XAA-PRO DIPEPTIDASE, PROLIDASE, DEINOCOCCUS RADIODURANS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KUMAR,V.ARE,B.GHOSH,S.JAMDAR,R.MAKDE REVDAT 2 04-JUL-18 5CDL 1 REMARK REVDAT 1 10-AUG-16 5CDL 0 JRNL AUTH A.KUMAR,V.ARE,B.GHOSH,S.JAMDAR,R.MAKDE JRNL TITL PROLINE DIPEPTIDASE FROM DEINOCOCCUS RADIODURANS JRNL TITL 2 (SELENOMETHIONINE DERIVATIVE) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 35666 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) : 0.177 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1785 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 45.1530 - 4.2309 0.99 2884 146 0.1588 0.1724 REMARK 3 2 4.2309 - 3.3585 1.00 2727 136 0.1487 0.1674 REMARK 3 3 3.3585 - 2.9340 1.00 2689 135 0.1762 0.2065 REMARK 3 4 2.9340 - 2.6658 1.00 2638 151 0.1894 0.2187 REMARK 3 5 2.6658 - 2.4748 1.00 2625 160 0.1862 0.2157 REMARK 3 6 2.4748 - 2.3289 1.00 2584 151 0.1818 0.1980 REMARK 3 7 2.3289 - 2.2122 1.00 2629 144 0.1735 0.1991 REMARK 3 8 2.2122 - 2.1159 1.00 2622 114 0.1699 0.2271 REMARK 3 9 2.1159 - 2.0345 1.00 2587 140 0.1854 0.1931 REMARK 3 10 2.0345 - 1.9643 1.00 2592 139 0.1947 0.2303 REMARK 3 11 1.9643 - 1.9029 1.00 2588 128 0.2191 0.2161 REMARK 3 12 1.9029 - 1.8485 0.95 2477 124 0.2381 0.2526 REMARK 3 13 1.8485 - 1.7998 0.86 2239 117 0.2703 0.2814 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.740 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 : 0.007 2656 REMARK 3 ANGLE : 1.084 3613 REMARK 3 CHIRALITY : 0.044 416 REMARK 3 PLANARITY : 0.005 478 REMARK 3 DIHEDRAL : 11.839 972 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 128 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.0527 13.3448 100.8410 REMARK 3 T TENSOR REMARK 3 T11: 0.0926 T22: 0.1106 REMARK 3 T33: 0.1196 T12: 0.0233 REMARK 3 T13: -0.0204 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 1.1788 L22: 1.3417 REMARK 3 L33: 2.0991 L12: 0.6345 REMARK 3 L13: 0.8215 L23: 0.6221 REMARK 3 S TENSOR REMARK 3 S11: 0.0906 S12: 0.1162 S13: -0.1433 REMARK 3 S21: 0.0426 S22: 0.0290 S23: -0.1038 REMARK 3 S31: 0.1756 S32: 0.0791 S33: -0.0972 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 129 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.9764 3.2462 90.3670 REMARK 3 T TENSOR REMARK 3 T11: 0.1049 T22: 0.1302 REMARK 3 T33: 0.0802 T12: 0.0033 REMARK 3 T13: -0.0043 T23: 0.0179 REMARK 3 L TENSOR REMARK 3 L11: 3.3873 L22: 1.4187 REMARK 3 L33: 1.3923 L12: -1.1408 REMARK 3 L13: -0.3888 L23: 0.3271 REMARK 3 S TENSOR REMARK 3 S11: -0.0408 S12: 0.1017 S13: 0.1074 REMARK 3 S21: 0.0713 S22: 0.0304 S23: 0.0299 REMARK 3 S31: -0.0005 S32: -0.2227 S33: 0.0169 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 206 THROUGH 285 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.0657 9.8504 75.6222 REMARK 3 T TENSOR REMARK 3 T11: 0.1081 T22: 0.1718 REMARK 3 T33: 0.1377 T12: 0.0395 REMARK 3 T13: 0.0013 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 0.7290 L22: 0.5050 REMARK 3 L33: 2.0567 L12: 0.5765 REMARK 3 L13: -0.4740 L23: -0.0782 REMARK 3 S TENSOR REMARK 3 S11: 0.0092 S12: 0.1495 S13: 0.1423 REMARK 3 S21: -0.0598 S22: 0.1202 S23: 0.1057 REMARK 3 S31: -0.1748 S32: -0.3338 S33: -0.0847 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 286 THROUGH 349 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7158 7.7999 78.9959 REMARK 3 T TENSOR REMARK 3 T11: 0.1147 T22: 0.1301 REMARK 3 T33: 0.0942 T12: 0.0218 REMARK 3 T13: 0.0027 T23: -0.0163 REMARK 3 L TENSOR REMARK 3 L11: 1.8714 L22: 1.0251 REMARK 3 L33: 1.7613 L12: 0.6875 REMARK 3 L13: -0.1979 L23: -0.4711 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: 0.0780 S13: 0.0687 REMARK 3 S21: 0.0174 S22: 0.0553 S23: 0.0057 REMARK 3 S31: -0.1548 S32: -0.1014 S33: -0.0240 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 5CDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211436. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : RRCAT INDUS-2 REMARK 200 BEAMLINE : PX-BL21 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978850 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL (SI111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35744 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 45.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.10300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.75500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: RESOLVE, SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5, 0.8M NAH2PO4, 0.8M REMARK 280 KH2PO4, PH 5.5, MICROBATCH, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 101.41200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.31600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.31600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 152.11800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.31600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.31600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.70600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.31600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.31600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 152.11800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.31600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.31600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 50.70600 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 101.41200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 202.82400 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 ARG A 85 CD NE CZ NH1 NH2 REMARK 470 HIS A 193 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 277 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 708 O HOH A 767 2.05 REMARK 500 O HOH A 540 O HOH A 794 2.15 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 568 O HOH A 681 7556 2.15 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 SER A 35 53.44 -113.64 REMARK 500 ARG A 117 -86.99 -104.47 REMARK 500 LEU A 297 68.81 -108.69 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 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 210 OD1 REMARK 620 2 ASP A 221 OD1 104.7 REMARK 620 3 MSE A 222 O 93.3 98.0 REMARK 620 4 THR A 223 OG1 88.1 163.4 70.3 REMARK 620 5 GLU A 328 OE1 173.8 77.3 92.2 91.2 REMARK 620 6 PO4 A 402 O1 93.4 95.4 163.0 94.3 80.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CDE RELATED DB: PDB REMARK 900 RELATED ID: 5CDV RELATED DB: PDB DBREF 5CDL A 1 349 UNP Q9RUY4 Q9RUY4_DEIRA 1 349 SEQADV 5CDL SER A 1 UNP Q9RUY4 MET 1 ENGINEERED MUTATION SEQRES 1 A 349 SER SER LYS MSE ASP GLN LEU ARG PRO VAL LEU GLY ARG SEQRES 2 A 349 ALA GLY VAL ASP ALA LEU TRP VAL SER ALA PRO ALA ASN SEQRES 3 A 349 VAL ARG TRP LEU SER GLY PHE THR SER ALA GLU ASP GLY SEQRES 4 A 349 LYS VAL LEU VAL SER PRO ASP GLY ALA THR LEU TYR THR SEQRES 5 A 349 ASP ALA ARG TYR THR VAL GLN ALA GLN GLU GLU SER SER SEQRES 6 A 349 LEU PRO GLN TYR ILE ALA ARG PRO PRO ALA THR TYR GLU SEQRES 7 A 349 HIS ALA ALA ASP THR VAL ARG GLY LEU ARG VAL GLY PHE SEQRES 8 A 349 GLU ALA GLU SER LEU THR VAL ALA GLU LEU GLU ASP LEU SEQRES 9 A 349 ARG GLN ALA TRP PRO ASN SER THR LEU VAL ALA LEU ARG SEQRES 10 A 349 GLY THR LEU GLY GLY LEU ARG ALA VAL LYS THR PRO GLU SEQRES 11 A 349 GLU ILE GLY ALA ILE ARG ALA ALA GLN ASP LEU ALA ASP SEQRES 12 A 349 ARG VAL TYR THR GLU VAL ARG PRO MSE ILE ARG ALA GLY SEQRES 13 A 349 VAL ARG GLU LEU ASP VAL ALA VAL GLU ILE GLU THR ARG SEQRES 14 A 349 LEU ARG ARG ALA GLY GLY GLU SER ALA PHE GLU LEU ILE SEQRES 15 A 349 VAL ALA SER GLY PRO ASN GLY ALA LYS PRO HIS GLY HIS SEQRES 16 A 349 ALA SER LYS ARG VAL ILE GLU ASP GLY ASP LEU VAL THR SEQRES 17 A 349 ILE ASP MSE GLY ALA ARG LEU GLY GLY TYR ASN SER ASP SEQRES 18 A 349 MSE THR ARG THR VAL ALA VAL GLY THR PRO SER ALA GLU SEQRES 19 A 349 MSE LYS ARG VAL TYR ASP ALA VAL LEU GLU ALA GLU GLU SEQRES 20 A 349 ALA ALA ILE ALA ALA ILE ARG PRO GLY VAL ARG ALA ALA SEQRES 21 A 349 ASP LEU ASP LYS LEU ALA ARG ASP LEU LEU THR ARG HIS SEQRES 22 A 349 GLY LEU GLY GLU ALA PHE ALA HIS SER LEU GLY HIS GLY SEQRES 23 A 349 VAL GLY LEU GLU VAL HIS GLU GLY PRO GLY LEU ARG GLY SEQRES 24 A 349 THR SER GLN ASP VAL LEU GLU ALA GLY MSE VAL ILE THR SEQRES 25 A 349 ILE GLU PRO GLY ALA TYR LEU PRO GLY VAL GLY GLY VAL SEQRES 26 A 349 ARG ILE GLU ASP LEU ILE LEU VAL THR GLU ASP GLY TYR SEQRES 27 A 349 GLU VAL LEU SER HIS SER ALA LYS GLU SER VAL MODRES 5CDL MSE A 4 MET MODIFIED RESIDUE MODRES 5CDL MSE A 152 MET MODIFIED RESIDUE MODRES 5CDL MSE A 211 MET MODIFIED RESIDUE MODRES 5CDL MSE A 222 MET MODIFIED RESIDUE MODRES 5CDL MSE A 235 MET MODIFIED RESIDUE MODRES 5CDL MSE A 309 MET MODIFIED RESIDUE HET MSE A 4 8 HET MSE A 152 8 HET MSE A 211 8 HET MSE A 222 8 HET MSE A 235 8 HET MSE A 309 8 HET MN A 401 1 HET PO4 A 402 5 HET PO4 A 403 5 HET PO4 A 404 5 HETNAM MSE SELENOMETHIONINE HETNAM MN MANGANESE (II) ION HETNAM PO4 PHOSPHATE ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 MN MN 2+ FORMUL 3 PO4 3(O4 P 3-) FORMUL 6 HOH *300(H2 O) HELIX 1 AA1 SER A 2 ALA A 14 1 13 HELIX 2 AA2 ALA A 23 GLY A 32 1 10 HELIX 3 AA3 SER A 35 GLU A 37 5 3 HELIX 4 AA4 TYR A 56 SER A 64 1 9 HELIX 5 AA5 PRO A 74 ALA A 81 1 8 HELIX 6 AA6 ASP A 82 ARG A 85 5 4 HELIX 7 AA7 THR A 97 TRP A 108 1 12 HELIX 8 AA8 ARG A 117 GLY A 121 5 5 HELIX 9 AA9 THR A 128 ARG A 150 1 23 HELIX 10 AB1 PRO A 151 ILE A 153 5 3 HELIX 11 AB2 ARG A 158 ALA A 173 1 16 HELIX 12 AB3 PRO A 187 LYS A 191 5 5 HELIX 13 AB4 SER A 232 ALA A 252 1 21 HELIX 14 AB5 ARG A 258 HIS A 273 1 16 SHEET 1 AA1 6 GLN A 68 ILE A 70 0 SHEET 2 AA1 6 GLY A 47 THR A 52 1 N LEU A 50 O TYR A 69 SHEET 3 AA1 6 GLY A 39 SER A 44 -1 N LYS A 40 O TYR A 51 SHEET 4 AA1 6 ALA A 18 VAL A 21 -1 N VAL A 21 O VAL A 41 SHEET 5 AA1 6 ARG A 88 GLU A 92 1 O GLY A 90 N ALA A 18 SHEET 6 AA1 6 THR A 112 LEU A 116 1 O VAL A 114 N VAL A 89 SHEET 1 AA2 3 GLU A 176 SER A 177 0 SHEET 2 AA2 3 ALA A 213 LEU A 215 -1 O ARG A 214 N GLU A 176 SHEET 3 AA2 3 TYR A 218 ASN A 219 -1 O TYR A 218 N LEU A 215 SHEET 1 AA3 3 ILE A 182 SER A 185 0 SHEET 2 AA3 3 LEU A 206 MSE A 211 -1 O THR A 208 N ALA A 184 SHEET 3 AA3 3 MSE A 222 ALA A 227 -1 O ARG A 224 N ILE A 209 SHEET 1 AA4 2 HIS A 285 GLY A 286 0 SHEET 2 AA4 2 GLU A 293 GLY A 296 -1 O PRO A 295 N GLY A 286 SHEET 1 AA5 3 VAL A 310 ILE A 313 0 SHEET 2 AA5 3 ASP A 329 THR A 334 -1 O ILE A 331 N ILE A 311 SHEET 3 AA5 3 GLY A 337 VAL A 340 -1 O GLU A 339 N LEU A 332 SHEET 1 AA6 2 GLY A 316 LEU A 319 0 SHEET 2 AA6 2 GLY A 323 ARG A 326 -1 O GLY A 323 N LEU A 319 LINK C LYS A 3 N MSE A 4 1555 1555 1.33 LINK C MSE A 4 N ASP A 5 1555 1555 1.33 LINK C PRO A 151 N MSE A 152 1555 1555 1.33 LINK C MSE A 152 N ILE A 153 1555 1555 1.33 LINK C ASP A 210 N MSE A 211 1555 1555 1.33 LINK OD1 ASP A 210 MN MN A 401 1555 1555 2.22 LINK C MSE A 211 N GLY A 212 1555 1555 1.33 LINK C ASP A 221 N MSE A 222 1555 1555 1.33 LINK OD1 ASP A 221 MN MN A 401 1555 1555 2.41 LINK C MSE A 222 N THR A 223 1555 1555 1.33 LINK O MSE A 222 MN MN A 401 1555 1555 2.73 LINK OG1 THR A 223 MN MN A 401 1555 1555 2.57 LINK C GLU A 234 N MSE A 235 1555 1555 1.33 LINK C MSE A 235 N LYS A 236 1555 1555 1.33 LINK C GLY A 308 N MSE A 309 1555 1555 1.33 LINK C MSE A 309 N VAL A 310 1555 1555 1.33 LINK OE1 GLU A 328 MN MN A 401 1555 1555 2.40 LINK MN MN A 401 O1 PO4 A 402 1555 1555 2.29 CISPEP 1 PRO A 73 PRO A 74 0 4.66 CISPEP 2 GLY A 294 PRO A 295 0 3.91 SITE 1 AC1 6 ASP A 210 ASP A 221 MSE A 222 THR A 223 SITE 2 AC1 6 GLU A 328 PO4 A 402 SITE 1 AC2 9 ASP A 210 ASP A 221 THR A 223 HIS A 285 SITE 2 AC2 9 HIS A 292 GLU A 314 GLU A 328 MN A 401 SITE 3 AC2 9 HOH A 700 SITE 1 AC3 8 GLY A 122 ARG A 124 GLU A 290 GLU A 293 SITE 2 AC3 8 GLY A 294 PO4 A 404 HOH A 516 HOH A 578 SITE 1 AC4 8 ASN A 26 GLU A 92 GLU A 94 LEU A 120 SITE 2 AC4 8 PO4 A 403 HOH A 516 HOH A 524 HOH A 577 CRYST1 60.632 60.632 202.824 90.00 90.00 90.00 P 43 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 0.016493 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004930 0.00000