HEADER HYDROLASE 30-JUN-20 6XMR TITLE X-RAY CRYSTALLOGRAPHIC STRUCTURE MODEL OF LACTOCOCCUS LACTIS PROLIDASE TITLE 2 MUTANT H38S COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOPEPTIDASE P FAMILY PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PEPTIDASE M24 FAMILY PROTEIN,PROLIDASE,XAA-PRO DIPEPTIDASE; COMPND 5 EC: 3.4.13.9; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS; SOURCE 3 ORGANISM_TAXID: 1358; SOURCE 4 GENE: PEPQ, AMHIJAGA_00052, BW151_08640, FNJ58_07375; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROLINE-SPECIFIC, ALLOSTERIC BEHAVIOUR, SUBSTRATE INHIBITION, KEYWDS 2 DIPEPTIDASE, LACTIC ACID BACTERIA, DEBITTERING OF FERMENTED FOODS, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.XU,P.GROCHULSKI,T.TANAKA REVDAT 2 18-OCT-23 6XMR 1 LINK REVDAT 1 15-JUL-20 6XMR 0 JRNL AUTH O.KGOSISEJO,J.A.CHEN,P.GROCHULSKI,T.TANAKA JRNL TITL CRYSTALLOGRAPHIC STRUCTURE OF RECOMBINANT LACTOCOCCUS LACTIS JRNL TITL 2 PROLIDASE TO SUPPORT PROPOSED STRUCTURE-FUNCTION JRNL TITL 3 RELATIONSHIPS. JRNL REF BIOCHIM BIOPHYS ACTA V.1865 473 2017 JRNL REF 2 PROTEINS PROTEOM JRNL REFN ISSN 1570-9639 JRNL PMID 28179139 JRNL DOI 10.1016/J.BBAPAP.2017.02.004 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 85753 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4298 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 5.2788 - 4.1912 1.00 2942 155 0.1222 0.1626 REMARK 3 2 4.1912 - 3.6618 1.00 2917 154 0.1377 0.1674 REMARK 3 3 3.6618 - 3.3272 1.00 2886 152 0.1438 0.1647 REMARK 3 4 3.3272 - 3.0888 1.00 2898 153 0.1495 0.1762 REMARK 3 5 3.0888 - 2.9067 1.00 2870 150 0.1601 0.1905 REMARK 3 6 2.9067 - 2.7612 0.99 2851 150 0.1690 0.2098 REMARK 3 7 2.7612 - 2.6410 0.99 2827 150 0.1671 0.2234 REMARK 3 8 2.6410 - 2.5393 0.98 2823 150 0.1733 0.1923 REMARK 3 9 2.5393 - 2.4517 0.99 2785 146 0.1658 0.1976 REMARK 3 10 2.4517 - 2.3751 0.99 2829 151 0.1636 0.1795 REMARK 3 11 2.3751 - 2.3072 0.98 2796 148 0.1622 0.2242 REMARK 3 12 2.3072 - 2.2464 0.98 2812 148 0.1701 0.2078 REMARK 3 13 2.2464 - 2.1916 0.97 2761 144 0.1625 0.1972 REMARK 3 14 2.1916 - 2.1418 0.98 2772 146 0.1624 0.1872 REMARK 3 15 2.1418 - 2.0962 0.97 2809 148 0.1619 0.2208 REMARK 3 16 2.0962 - 2.0543 0.97 2723 142 0.1619 0.1795 REMARK 3 17 2.0543 - 2.0155 0.95 2738 142 0.1694 0.2171 REMARK 3 18 2.0155 - 1.9796 0.96 2690 141 0.1764 0.2181 REMARK 3 19 1.9796 - 1.9460 0.93 2643 141 0.1802 0.2167 REMARK 3 20 1.9460 - 1.9146 0.94 2678 141 0.1951 0.2705 REMARK 3 21 1.9146 - 1.8851 0.92 2585 143 0.2061 0.2325 REMARK 3 22 1.8851 - 1.8574 0.91 2602 134 0.2109 0.2557 REMARK 3 23 1.8574 - 1.8313 0.90 2558 135 0.2158 0.2904 REMARK 3 24 1.8313 - 1.8065 0.89 2511 131 0.2172 0.2349 REMARK 3 25 1.8065 - 1.7831 0.88 2494 128 0.2234 0.2757 REMARK 3 26 1.7831 - 1.7608 0.88 2465 130 0.2330 0.2578 REMARK 3 27 1.7608 - 1.7396 0.85 2409 132 0.2357 0.2622 REMARK 3 28 1.7396 - 1.7193 0.85 2386 126 0.2538 0.2913 REMARK 3 29 1.7193 - 1.7000 0.81 2319 124 0.2760 0.3276 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) : 19.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.38 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 32.4357 -1.0123 -16.1359 REMARK 3 T TENSOR REMARK 3 T11: 0.1168 T22: 0.1060 REMARK 3 T33: 0.1191 T12: -0.0027 REMARK 3 T13: -0.0009 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.1416 L22: 0.0941 REMARK 3 L33: 0.1573 L12: -0.0100 REMARK 3 L13: -0.0537 L23: -0.0911 REMARK 3 S TENSOR REMARK 3 S11: 0.0023 S12: 0.0094 S13: 0.0096 REMARK 3 S21: 0.0125 S22: -0.0070 S23: 0.0061 REMARK 3 S31: -0.0114 S32: 0.0090 S33: 0.0044 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 2190 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XMR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000249759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97935 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93477 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 41.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.180 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.45 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: PHASER 2.8.2 REMARK 200 STARTING MODEL: PDB ENTRY 4ZNG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CALCIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 PROPANE, 12-15% W/V PEG4000, PH 6.7, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277.15K. 0.1 M CALCIUM ACETATE, 0.1 M BIS-TRIS REMARK 280 PROPANE, 12-15% W/V PEG3350, PH 6.75, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 40.38000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.80000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.85500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.80000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.38000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.85500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 ASP A 148 O HOH A 501 1.81 REMARK 500 O HOH A 709 O HOH A 847 2.01 REMARK 500 O HOH B 896 O HOH B 960 2.12 REMARK 500 O MET B 1 O HOH B 501 2.12 REMARK 500 O HOH A 973 O HOH A 1049 2.14 REMARK 500 O HOH A 872 O HOH A 1113 2.14 REMARK 500 O HOH B 867 O HOH B 875 2.16 REMARK 500 O HOH A 510 O HOH A 511 2.16 REMARK 500 O HOH A 505 O HOH A 529 2.16 REMARK 500 O HOH B 821 O HOH B 873 2.17 REMARK 500 O HOH A 526 O HOH A 915 2.17 REMARK 500 O HOH A 510 O HOH A 640 2.18 REMARK 500 O HOH B 817 O HOH B 1041 2.19 REMARK 500 O HOH B 1081 O HOH B 1106 2.19 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 872 O HOH B 528 3644 2.10 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 GLU B 62 CA - CB - CG ANGL. DEV. = 13.3 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 SER A 38 -118.83 68.61 REMARK 500 ASP A 49 58.83 -154.81 REMARK 500 ARG A 164 -127.97 54.85 REMARK 500 GLU A 304 -156.10 -138.67 REMARK 500 LYS A 333 -64.87 -125.00 REMARK 500 SER B 38 -121.94 67.62 REMARK 500 ASP B 49 62.08 -156.91 REMARK 500 SER B 92 156.07 63.72 REMARK 500 ARG B 164 -126.79 55.36 REMARK 500 LYS B 333 -65.69 -124.21 REMARK 500 ASN B 347 19.04 -140.85 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 SER B 92 ASP B 93 -39.10 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 A1124 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A1125 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A1126 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A1127 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A1128 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A1129 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A1130 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A1131 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A1132 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A1133 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A1134 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A1135 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A1136 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A1137 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A1138 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A1139 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH A1140 DISTANCE = 8.66 ANGSTROMS REMARK 525 HOH B1089 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH B1090 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH B1091 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B1092 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH B1093 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH B1094 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH B1095 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH B1096 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH B1097 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH B1098 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH B1099 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH B1100 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH B1101 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH B1102 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH B1103 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH B1104 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH B1105 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH B1106 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH B1107 DISTANCE = 7.18 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 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 221 OD1 REMARK 620 2 ASP A 221 OD2 55.1 REMARK 620 3 ASP A 232 OD1 99.1 152.7 REMARK 620 4 GLU A 339 OE1 102.6 104.9 88.3 REMARK 620 5 HOH A 521 O 143.7 88.7 116.3 87.1 REMARK 620 6 HOH A 831 O 95.2 86.3 87.6 162.1 79.1 REMARK 620 N 1 2 3 4 5 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 232 OD2 REMARK 620 2 HIS A 296 NE2 91.6 REMARK 620 3 GLU A 325 OE2 155.3 82.5 REMARK 620 4 GLU A 339 OE2 85.3 124.0 78.3 REMARK 620 5 HOH A 521 O 109.8 143.9 88.0 87.5 REMARK 620 6 HOH A 730 O 95.6 81.0 107.1 154.9 68.6 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 ASP B 221 OD1 REMARK 620 2 ASP B 221 OD2 56.7 REMARK 620 3 ASP B 232 OD1 95.0 150.8 REMARK 620 4 GLU B 339 OE1 100.8 104.1 87.2 REMARK 620 5 HOH B 544 O 146.5 89.8 118.0 87.1 REMARK 620 6 HOH B 866 O 97.9 86.0 91.3 161.3 77.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 232 OD2 REMARK 620 2 HIS B 296 NE2 91.4 REMARK 620 3 GLU B 325 OE2 156.6 84.3 REMARK 620 4 GLU B 339 OE2 84.6 119.8 77.7 REMARK 620 5 HOH B 544 O 105.7 151.2 88.2 85.4 REMARK 620 6 HOH B 658 O 89.9 84.1 112.4 155.5 73.1 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 MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZNG RELATED DB: PDB REMARK 900 WILD TYPE PROLIDASE DBREF 6XMR A 1 362 UNP A8WBX8 A8WBX8_9LACT 1 362 DBREF 6XMR B 1 362 UNP A8WBX8 A8WBX8_9LACT 1 362 SEQADV 6XMR SER A 38 UNP A8WBX8 HIS 38 ENGINEERED MUTATION SEQADV 6XMR SER B 38 UNP A8WBX8 HIS 38 ENGINEERED MUTATION SEQRES 1 A 362 MET SER LYS ILE GLU ARG ILE SER ALA PHE LEU ASN ASP SEQRES 2 A 362 LYS GLU VAL ASP MET THR PHE ILE THR ASN PRO THR THR SEQRES 3 A 362 LEU ASN TYR LEU THR GLY LEU ALA ILE ASP PRO SER GLU SEQRES 4 A 362 ARG ILE ALA GLY LEU MET ILE PHE ARG ASP SER THR PRO SEQRES 5 A 362 MET LEU PHE THR PRO ALA LEU GLU VAL GLU LYS ALA LYS SEQRES 6 A 362 GLU HIS THR SER GLY LEU ASP ILE PHE GLY TYR GLU ASP SEQRES 7 A 362 SER GLN ASN PRO TRP GLU VAL VAL LYS ASN HIS VAL LYS SEQRES 8 A 362 SER ASP VAL LYS SER ILE ALA VAL GLU PHE SER ASP ILE SEQRES 9 A 362 PRO LEU ALA LYS THR GLU GLY LEU LYS ALA GLN PHE GLY SEQRES 10 A 362 ASP ILE ASN PHE VAL ASN LEU THR PRO LEU ILE GLU ARG SEQRES 11 A 362 MET ARG LEU ILE LYS SER ALA ASP GLU ILE GLU LYS MET SEQRES 12 A 362 LYS VAL ALA GLY ASP PHE ALA ASP LYS CYS PHE GLU ILE SEQRES 13 A 362 GLY PHE ALA THR ALA ALA GLU ARG ASN GLY VAL THR GLU SEQRES 14 A 362 SER ASP ILE VAL ALA LYS ILE GLU TYR GLU MET LYS ARG SEQRES 15 A 362 MET GLY VAL PRO GLN MET SER PHE ASP THR LEU VAL LEU SEQRES 16 A 362 SER GLY ALA ARG ALA ALA ASN PRO HIS GLY ALA PRO GLU SEQRES 17 A 362 ASN VAL GLU ILE GLN GLU ASN LYS LEU LEU LEU PHE ASP SEQRES 18 A 362 LEU GLY VAL MET SER GLY GLY TYR ALA SER ASP ALA THR SEQRES 19 A 362 ARG THR ILE ALA ILE GLY GLN PRO ASN ASP PHE ASP ALA SEQRES 20 A 362 GLU ILE HIS LYS ILE VAL LYS GLU ALA GLN GLN ALA ALA SEQRES 21 A 362 MET ASP PHE ILE LYS PRO GLY VAL THR ALA HIS GLU VAL SEQRES 22 A 362 ASP ALA VAL ALA ARG ASP LEU ILE THR LYS ALA GLY TYR SEQRES 23 A 362 GLY GLU TYR PHE ASN HIS ARG LEU GLY HIS GLY ILE GLY SEQRES 24 A 362 MET ASP VAL HIS GLU TYR PRO SER ILE VAL ALA GLY ASN SEQRES 25 A 362 ASP LEU VAL ILE GLN GLU GLY MET CYS PHE SER ASN GLU SEQRES 26 A 362 PRO GLY ILE TYR ILE PRO GLY LYS VAL GLY VAL ARG ILE SEQRES 27 A 362 GLU ASP CYS LEU TYR VAL THR GLU ASN GLY CYS GLU SER SEQRES 28 A 362 PHE THR HIS THR ASP HIS ASP LEU LEU ILE PHE SEQRES 1 B 362 MET SER LYS ILE GLU ARG ILE SER ALA PHE LEU ASN ASP SEQRES 2 B 362 LYS GLU VAL ASP MET THR PHE ILE THR ASN PRO THR THR SEQRES 3 B 362 LEU ASN TYR LEU THR GLY LEU ALA ILE ASP PRO SER GLU SEQRES 4 B 362 ARG ILE ALA GLY LEU MET ILE PHE ARG ASP SER THR PRO SEQRES 5 B 362 MET LEU PHE THR PRO ALA LEU GLU VAL GLU LYS ALA LYS SEQRES 6 B 362 GLU HIS THR SER GLY LEU ASP ILE PHE GLY TYR GLU ASP SEQRES 7 B 362 SER GLN ASN PRO TRP GLU VAL VAL LYS ASN HIS VAL LYS SEQRES 8 B 362 SER ASP VAL LYS SER ILE ALA VAL GLU PHE SER ASP ILE SEQRES 9 B 362 PRO LEU ALA LYS THR GLU GLY LEU LYS ALA GLN PHE GLY SEQRES 10 B 362 ASP ILE ASN PHE VAL ASN LEU THR PRO LEU ILE GLU ARG SEQRES 11 B 362 MET ARG LEU ILE LYS SER ALA ASP GLU ILE GLU LYS MET SEQRES 12 B 362 LYS VAL ALA GLY ASP PHE ALA ASP LYS CYS PHE GLU ILE SEQRES 13 B 362 GLY PHE ALA THR ALA ALA GLU ARG ASN GLY VAL THR GLU SEQRES 14 B 362 SER ASP ILE VAL ALA LYS ILE GLU TYR GLU MET LYS ARG SEQRES 15 B 362 MET GLY VAL PRO GLN MET SER PHE ASP THR LEU VAL LEU SEQRES 16 B 362 SER GLY ALA ARG ALA ALA ASN PRO HIS GLY ALA PRO GLU SEQRES 17 B 362 ASN VAL GLU ILE GLN GLU ASN LYS LEU LEU LEU PHE ASP SEQRES 18 B 362 LEU GLY VAL MET SER GLY GLY TYR ALA SER ASP ALA THR SEQRES 19 B 362 ARG THR ILE ALA ILE GLY GLN PRO ASN ASP PHE ASP ALA SEQRES 20 B 362 GLU ILE HIS LYS ILE VAL LYS GLU ALA GLN GLN ALA ALA SEQRES 21 B 362 MET ASP PHE ILE LYS PRO GLY VAL THR ALA HIS GLU VAL SEQRES 22 B 362 ASP ALA VAL ALA ARG ASP LEU ILE THR LYS ALA GLY TYR SEQRES 23 B 362 GLY GLU TYR PHE ASN HIS ARG LEU GLY HIS GLY ILE GLY SEQRES 24 B 362 MET ASP VAL HIS GLU TYR PRO SER ILE VAL ALA GLY ASN SEQRES 25 B 362 ASP LEU VAL ILE GLN GLU GLY MET CYS PHE SER ASN GLU SEQRES 26 B 362 PRO GLY ILE TYR ILE PRO GLY LYS VAL GLY VAL ARG ILE SEQRES 27 B 362 GLU ASP CYS LEU TYR VAL THR GLU ASN GLY CYS GLU SER SEQRES 28 B 362 PHE THR HIS THR ASP HIS ASP LEU LEU ILE PHE HET MN A 401 1 HET MN A 402 1 HET MN B 401 1 HET MN B 402 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 4(MN 2+) FORMUL 7 HOH *1247(H2 O) HELIX 1 AA1 SER A 2 GLU A 15 1 14 HELIX 2 AA2 ASN A 23 GLY A 32 1 10 HELIX 3 AA3 GLU A 60 HIS A 67 1 8 HELIX 4 AA4 ASN A 81 VAL A 90 1 10 HELIX 5 AA5 PRO A 105 GLY A 117 1 13 HELIX 6 AA6 LEU A 124 LEU A 133 1 10 HELIX 7 AA7 SER A 136 GLU A 163 1 28 HELIX 8 AA8 THR A 168 MET A 183 1 16 HELIX 9 AA9 ALA A 198 ASN A 202 5 5 HELIX 10 AB1 ASN A 243 ILE A 264 1 22 HELIX 11 AB2 THR A 269 GLY A 285 1 17 HELIX 12 AB3 TYR A 286 PHE A 290 5 5 HELIX 13 AB4 SER B 2 GLU B 15 1 14 HELIX 14 AB5 ASN B 23 GLY B 32 1 10 HELIX 15 AB6 GLU B 60 THR B 68 1 9 HELIX 16 AB7 ASN B 81 VAL B 90 1 10 HELIX 17 AB8 PRO B 105 GLY B 117 1 13 HELIX 18 AB9 LEU B 124 LEU B 133 1 10 HELIX 19 AC1 SER B 136 GLU B 163 1 28 HELIX 20 AC2 THR B 168 MET B 183 1 16 HELIX 21 AC3 ALA B 198 ASN B 202 5 5 HELIX 22 AC4 ASN B 243 ILE B 264 1 22 HELIX 23 AC5 THR B 269 ALA B 284 1 16 HELIX 24 AC6 TYR B 286 PHE B 290 5 5 SHEET 1 AA1 3 MET A 18 THR A 19 0 SHEET 2 AA1 3 SER A 96 VAL A 99 1 O ALA A 98 N MET A 18 SHEET 3 AA1 3 ASN A 120 ASN A 123 1 O VAL A 122 N VAL A 99 SHEET 1 AA2 3 GLY A 43 MET A 45 0 SHEET 2 AA2 3 MET A 53 PRO A 57 -1 O MET A 53 N MET A 45 SHEET 3 AA2 3 ASP A 72 TYR A 76 1 O ASP A 72 N LEU A 54 SHEET 1 AA3 3 LEU A 193 SER A 196 0 SHEET 2 AA3 3 LYS A 216 LEU A 222 -1 O ASP A 221 N LEU A 193 SHEET 3 AA3 3 ALA A 233 ILE A 239 -1 O ARG A 235 N PHE A 220 SHEET 1 AA4 2 MET A 225 SER A 226 0 SHEET 2 AA4 2 TYR A 229 ALA A 230 -1 O TYR A 229 N SER A 226 SHEET 1 AA5 2 GLY A 295 GLY A 297 0 SHEET 2 AA5 2 GLU A 304 ILE A 308 -1 O ILE A 308 N GLY A 295 SHEET 1 AA6 3 CYS A 321 ASN A 324 0 SHEET 2 AA6 3 ASP A 340 THR A 345 -1 O LEU A 342 N PHE A 322 SHEET 3 AA6 3 GLY A 348 SER A 351 -1 O GLU A 350 N TYR A 343 SHEET 1 AA7 2 GLY A 327 ILE A 330 0 SHEET 2 AA7 2 VAL A 334 ARG A 337 -1 O VAL A 334 N ILE A 330 SHEET 1 AA8 3 MET B 18 THR B 19 0 SHEET 2 AA8 3 SER B 96 VAL B 99 1 O ALA B 98 N MET B 18 SHEET 3 AA8 3 ASN B 120 ASN B 123 1 O VAL B 122 N VAL B 99 SHEET 1 AA9 3 GLY B 43 MET B 45 0 SHEET 2 AA9 3 MET B 53 PRO B 57 -1 O MET B 53 N MET B 45 SHEET 3 AA9 3 ASP B 72 TYR B 76 1 O PHE B 74 N LEU B 54 SHEET 1 AB1 3 GLN B 187 MET B 188 0 SHEET 2 AB1 3 VAL B 224 SER B 226 -1 O MET B 225 N GLN B 187 SHEET 3 AB1 3 TYR B 229 ALA B 230 -1 O TYR B 229 N SER B 226 SHEET 1 AB2 3 LEU B 193 SER B 196 0 SHEET 2 AB2 3 LYS B 216 LEU B 222 -1 O ASP B 221 N LEU B 193 SHEET 3 AB2 3 ALA B 233 ILE B 239 -1 O ARG B 235 N PHE B 220 SHEET 1 AB3 2 GLY B 295 GLY B 297 0 SHEET 2 AB3 2 GLU B 304 ILE B 308 -1 O ILE B 308 N GLY B 295 SHEET 1 AB4 3 CYS B 321 ASN B 324 0 SHEET 2 AB4 3 ASP B 340 VAL B 344 -1 O ASP B 340 N ASN B 324 SHEET 3 AB4 3 CYS B 349 SER B 351 -1 O GLU B 350 N TYR B 343 SHEET 1 AB5 2 GLY B 327 ILE B 330 0 SHEET 2 AB5 2 VAL B 334 ARG B 337 -1 O VAL B 334 N ILE B 330 LINK OD1 ASP A 221 MN MN A 402 1555 1555 2.09 LINK OD2 ASP A 221 MN MN A 402 1555 1555 2.54 LINK OD2 ASP A 232 MN MN A 401 1555 1555 2.17 LINK OD1 ASP A 232 MN MN A 402 1555 1555 2.09 LINK NE2 HIS A 296 MN MN A 401 1555 1555 2.12 LINK OE2 GLU A 325 MN MN A 401 1555 1555 2.29 LINK OE2 GLU A 339 MN MN A 401 1555 1555 2.18 LINK OE1 GLU A 339 MN MN A 402 1555 1555 2.15 LINK MN MN A 401 O HOH A 521 1555 1555 2.20 LINK MN MN A 401 O HOH A 730 1555 1555 2.25 LINK MN MN A 402 O HOH A 521 1555 1555 2.24 LINK MN MN A 402 O HOH A 831 1555 1555 2.33 LINK OD1 ASP B 221 MN MN B 401 1555 1555 2.12 LINK OD2 ASP B 221 MN MN B 401 1555 1555 2.45 LINK OD1 ASP B 232 MN MN B 401 1555 1555 2.14 LINK OD2 ASP B 232 MN MN B 402 1555 1555 2.14 LINK NE2 HIS B 296 MN MN B 402 1555 1555 2.15 LINK OE2 GLU B 325 MN MN B 402 1555 1555 2.32 LINK OE1 GLU B 339 MN MN B 401 1555 1555 2.16 LINK OE2 GLU B 339 MN MN B 402 1555 1555 2.19 LINK MN MN B 401 O HOH B 544 1555 1555 2.12 LINK MN MN B 401 O HOH B 866 1555 1555 2.23 LINK MN MN B 402 O HOH B 544 1555 1555 2.30 LINK MN MN B 402 O HOH B 658 1555 1555 2.29 CISPEP 1 TYR A 305 PRO A 306 0 6.76 CISPEP 2 TYR B 305 PRO B 306 0 3.64 SITE 1 AC1 7 ASP A 232 HIS A 296 GLU A 325 GLU A 339 SITE 2 AC1 7 MN A 402 HOH A 521 HOH A 730 SITE 1 AC2 7 ASP A 221 ASP A 232 THR A 234 GLU A 339 SITE 2 AC2 7 MN A 401 HOH A 521 HOH A 831 SITE 1 AC3 7 ASP B 221 ASP B 232 THR B 234 GLU B 339 SITE 2 AC3 7 MN B 402 HOH B 544 HOH B 866 SITE 1 AC4 7 ASP B 232 HIS B 296 GLU B 325 GLU B 339 SITE 2 AC4 7 MN B 401 HOH B 544 HOH B 658 CRYST1 80.760 85.710 117.600 90.00 90.00 90.00 P 21 21 21 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 0.012382 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008503 0.00000