HEADER HYDROLASE 24-MAR-19 6R4W TITLE CRYSTAL STRUCTURE OF APO PPEP-1(E143A/Y178F) IN COMPLEX WITH SUBSTRATE TITLE 2 PEPTIDE AC-EVNAPVP-CONH2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRO-PRO ENDOPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PPEP-1,ZINC METALLOPROTEASE ZMP1; COMPND 5 EC: 3.4.24.89; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ACE-GLU-VAL-ASN-ALA-PRO-VAL-LPD; COMPND 9 CHAIN: C, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PEPTOCLOSTRIDIUM DIFFICILE; SOURCE 3 ORGANISM_TAXID: 1496; SOURCE 4 GENE: ZMP1, PPEP-1, CD630_28300; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: CLOSTRIDIOIDES DIFFICILE; SOURCE 11 ORGANISM_TAXID: 1496 KEYWDS PRO-PRO ENDOPEPTIDASE 1, ZINC METALLOPEPTIDASE, CLOSTRIDIUM KEYWDS 2 DIFFICILE, VIRULENCE FACTOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.PICHLO,U.BAUMANN REVDAT 4 24-JAN-24 6R4W 1 LINK REVDAT 3 07-AUG-19 6R4W 1 JRNL REVDAT 2 26-JUN-19 6R4W 1 JRNL REVDAT 1 12-JUN-19 6R4W 0 JRNL AUTH C.PICHLO,L.JUETTEN,F.WOJTALLA,M.SCHACHERL,D.DIAZ,U.BAUMANN JRNL TITL MOLECULAR DETERMINANTS OF THE MECHANISM AND SUBSTRATE JRNL TITL 2 SPECIFICITY OFCLOSTRIDIUM DIFFICILEPROLINE-PROLINE JRNL TITL 3 ENDOPEPTIDASE-1. JRNL REF J.BIOL.CHEM. V. 294 11525 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31182482 JRNL DOI 10.1074/JBC.RA119.009029 REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_3395: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 77691 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2023 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 40.8890 - 3.3526 0.99 5562 151 0.1407 0.1547 REMARK 3 2 3.3526 - 2.6612 0.99 5442 146 0.1538 0.1689 REMARK 3 3 2.6612 - 2.3248 1.00 5479 149 0.1529 0.1700 REMARK 3 4 2.3248 - 2.1123 1.00 5446 137 0.1426 0.1762 REMARK 3 5 2.1123 - 1.9609 1.00 5406 151 0.1493 0.1630 REMARK 3 6 1.9609 - 1.8453 1.00 5435 147 0.1604 0.2046 REMARK 3 7 1.8453 - 1.7529 1.00 5464 140 0.1727 0.2178 REMARK 3 8 1.7529 - 1.6766 0.99 5337 143 0.2351 0.2800 REMARK 3 9 1.6766 - 1.6120 0.99 5372 148 0.2317 0.2668 REMARK 3 10 1.6120 - 1.5564 0.99 5361 138 0.2036 0.2132 REMARK 3 11 1.5564 - 1.5077 1.00 5433 141 0.2146 0.2289 REMARK 3 12 1.5077 - 1.4646 1.00 5372 150 0.2595 0.2640 REMARK 3 13 1.4646 - 1.4261 0.99 5356 138 0.2812 0.2703 REMARK 3 14 1.4261 - 1.3913 0.97 5203 144 0.2905 0.3130 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.740 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 : 0.008 3306 REMARK 3 ANGLE : 0.919 4497 REMARK 3 CHIRALITY : 0.071 494 REMARK 3 PLANARITY : 0.007 594 REMARK 3 DIHEDRAL : 11.882 1223 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 26 THROUGH 157) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3641 14.9805 -12.2274 REMARK 3 T TENSOR REMARK 3 T11: 0.0976 T22: 0.1119 REMARK 3 T33: 0.1012 T12: 0.0044 REMARK 3 T13: 0.0034 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.9665 L22: 1.4292 REMARK 3 L33: 1.5950 L12: -0.0632 REMARK 3 L13: 0.0015 L23: 0.2046 REMARK 3 S TENSOR REMARK 3 S11: 0.0494 S12: -0.0012 S13: 0.0189 REMARK 3 S21: 0.1050 S22: -0.0278 S23: 0.0072 REMARK 3 S31: -0.0079 S32: 0.0323 S33: -0.0022 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 158 THROUGH 220) REMARK 3 ORIGIN FOR THE GROUP (A): -6.6857 0.2989 -20.2363 REMARK 3 T TENSOR REMARK 3 T11: 0.1974 T22: 0.1319 REMARK 3 T33: 0.1374 T12: -0.0049 REMARK 3 T13: -0.0341 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.9545 L22: 1.3247 REMARK 3 L33: 0.9334 L12: -0.1306 REMARK 3 L13: 0.0945 L23: 0.2180 REMARK 3 S TENSOR REMARK 3 S11: 0.0162 S12: 0.0589 S13: -0.1058 REMARK 3 S21: -0.1714 S22: -0.0212 S23: 0.2218 REMARK 3 S31: 0.3263 S32: -0.0746 S33: -0.0011 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 29 THROUGH 131) REMARK 3 ORIGIN FOR THE GROUP (A): -18.6170 12.8844 -52.1170 REMARK 3 T TENSOR REMARK 3 T11: 0.0969 T22: 0.1230 REMARK 3 T33: 0.1073 T12: 0.0015 REMARK 3 T13: 0.0075 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 1.4069 L22: 1.0203 REMARK 3 L33: 1.3280 L12: 0.0325 REMARK 3 L13: -0.0113 L23: 0.1606 REMARK 3 S TENSOR REMARK 3 S11: 0.0716 S12: -0.0139 S13: 0.0408 REMARK 3 S21: 0.0285 S22: -0.0097 S23: -0.0324 REMARK 3 S31: -0.0418 S32: -0.0889 S33: -0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 132 THROUGH 220) REMARK 3 ORIGIN FOR THE GROUP (A): -17.2158 -2.0275 -42.7848 REMARK 3 T TENSOR REMARK 3 T11: 0.2181 T22: 0.1176 REMARK 3 T33: 0.1296 T12: -0.0152 REMARK 3 T13: -0.0221 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 1.3960 L22: 1.4825 REMARK 3 L33: 1.2002 L12: 0.1312 REMARK 3 L13: 0.6203 L23: -0.2259 REMARK 3 S TENSOR REMARK 3 S11: 0.1803 S12: -0.0633 S13: -0.1802 REMARK 3 S21: 0.2924 S22: -0.0630 S23: 0.0609 REMARK 3 S31: 0.2863 S32: -0.0532 S33: 0.0051 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' REMARK 3 ORIGIN FOR THE GROUP (A): -26.9480 6.3150 -46.5096 REMARK 3 T TENSOR REMARK 3 T11: 0.2805 T22: 0.3080 REMARK 3 T33: 0.2326 T12: -0.0735 REMARK 3 T13: 0.0728 T23: -0.0522 REMARK 3 L TENSOR REMARK 3 L11: 1.0912 L22: 1.9086 REMARK 3 L33: 0.7412 L12: -0.8054 REMARK 3 L13: 0.6042 L23: -1.1693 REMARK 3 S TENSOR REMARK 3 S11: 0.0495 S12: 0.4774 S13: -0.2653 REMARK 3 S21: -0.3364 S22: 0.2233 S23: 0.1193 REMARK 3 S31: 0.1650 S32: -0.3086 S33: 0.4481 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' REMARK 3 ORIGIN FOR THE GROUP (A): 6.1566 9.6845 -20.4762 REMARK 3 T TENSOR REMARK 3 T11: 0.1676 T22: 0.2065 REMARK 3 T33: 0.2062 T12: 0.0171 REMARK 3 T13: -0.0119 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.0842 L22: 0.0649 REMARK 3 L33: 0.0574 L12: 0.0454 REMARK 3 L13: -0.0431 L23: 0.0143 REMARK 3 S TENSOR REMARK 3 S11: 0.1242 S12: 0.1040 S13: -0.3668 REMARK 3 S21: -0.1500 S22: 0.0577 S23: -0.1307 REMARK 3 S31: 0.0921 S32: 0.2563 S33: 0.0002 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 6R4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292100803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20160617 REMARK 200 DATA SCALING SOFTWARE : XDS 20160617 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77720 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 40.871 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5A0P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 MICROL 12 MG PER ML RPPEP-1 E143A REMARK 280 Y178F WITH 6 MM SUBSTRATE PEPTIDE IN 20 MM TRIS PH 7.5, 200 MM REMARK 280 NACL WAS MIXED WITH 1.5 MICROL PRECIPITANT SOLUTION CONTAINING: REMARK 280 100 MM TRIS PH 8.0, 2.25 M AMMONIUM PHOSPHATE DIBASIC. RESERVOIR REMARK 280 VOLUME: 200 MICROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 21.46150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 REMARK 350 BIOMOLECULE: 2 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: 1800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 23 REMARK 465 SER A 24 REMARK 465 HIS A 25 REMARK 465 GLY B 23 REMARK 465 SER B 24 REMARK 465 HIS B 25 REMARK 465 MET B 26 REMARK 465 ASP B 27 REMARK 465 SER B 28 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 MET A 26 CG SD CE 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 HD21 ASN A 63 O HOH A 405 1.57 REMARK 500 OD2 ASP B 88 O HOH B 401 2.02 REMARK 500 O HOH B 532 O HOH B 580 2.03 REMARK 500 O HOH B 515 O HOH B 554 2.04 REMARK 500 O HOH A 593 O HOH A 613 2.05 REMARK 500 O LYS B 220 O HOH B 402 2.13 REMARK 500 NZ LYS A 51 O HOH A 401 2.14 REMARK 500 OE2 GLU B 185 O HOH B 403 2.15 REMARK 500 O HOH A 437 O HOH A 444 2.18 REMARK 500 OD1 ASN B 129 O HOH B 404 2.18 REMARK 500 NZ LYS A 130 O HOH A 402 2.18 REMARK 500 O HOH A 549 O HOH A 568 2.18 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 B 492 O HOH B 553 1545 1.94 REMARK 500 O HOH A 506 O HOH A 549 2555 2.03 REMARK 500 O HOH A 587 O HOH A 610 1455 2.06 REMARK 500 O HOH B 412 O HOH B 577 2454 2.13 REMARK 500 O HOH B 557 O HOH B 564 2454 2.14 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 178 -65.19 -120.13 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 142 NE2 REMARK 620 2 HIS A 146 NE2 98.0 REMARK 620 3 GLU A 185 OE1 99.3 84.1 REMARK 620 4 ALA D 122 O 103.6 142.6 121.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 142 NE2 REMARK 620 2 HIS B 146 NE2 95.4 REMARK 620 3 GLU B 185 OE1 101.6 92.1 REMARK 620 4 ALA C 4 O 116.3 129.1 116.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ACE C 0 and GLU C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide VAL C 6 and LPD C 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ACE D 0 and GLU D REMARK 800 119 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide VAL D 124 and LPD D REMARK 800 125 DBREF 6R4W A 27 220 UNP Q183R7 PPEP1_PEPD6 27 220 DBREF 6R4W B 27 220 UNP Q183R7 PPEP1_PEPD6 27 220 DBREF 6R4W C 0 7 PDB 6R4W 6R4W 0 7 DBREF 6R4W D 0 125 PDB 6R4W 6R4W 0 125 SEQADV 6R4W GLY A 23 UNP Q183R7 EXPRESSION TAG SEQADV 6R4W SER A 24 UNP Q183R7 EXPRESSION TAG SEQADV 6R4W HIS A 25 UNP Q183R7 EXPRESSION TAG SEQADV 6R4W MET A 26 UNP Q183R7 EXPRESSION TAG SEQADV 6R4W ALA A 143 UNP Q183R7 GLU 143 CONFLICT SEQADV 6R4W PHE A 178 UNP Q183R7 TYR 178 CONFLICT SEQADV 6R4W GLY B 23 UNP Q183R7 EXPRESSION TAG SEQADV 6R4W SER B 24 UNP Q183R7 EXPRESSION TAG SEQADV 6R4W HIS B 25 UNP Q183R7 EXPRESSION TAG SEQADV 6R4W MET B 26 UNP Q183R7 EXPRESSION TAG SEQADV 6R4W ALA B 143 UNP Q183R7 GLU 143 CONFLICT SEQADV 6R4W PHE B 178 UNP Q183R7 TYR 178 CONFLICT SEQRES 1 A 198 GLY SER HIS MET ASP SER THR THR ILE GLN GLN ASN LYS SEQRES 2 A 198 ASP THR LEU SER GLN ILE VAL VAL PHE PRO THR GLY ASN SEQRES 3 A 198 TYR ASP LYS ASN GLU ALA ASN ALA MET VAL ASN ARG LEU SEQRES 4 A 198 ALA ASN ILE ASP GLY LYS TYR LEU ASN ALA LEU LYS GLN SEQRES 5 A 198 ASN ASN LEU LYS ILE LYS LEU LEU SER GLY LYS LEU THR SEQRES 6 A 198 ASP GLU LYS GLU TYR ALA TYR LEU LYS GLY VAL VAL PRO SEQRES 7 A 198 LYS GLY TRP GLU GLY THR GLY LYS THR TRP ASP ASP VAL SEQRES 8 A 198 PRO GLY LEU GLY GLY SER THR VAL ALA LEU ARG ILE GLY SEQRES 9 A 198 PHE SER ASN LYS GLY LYS GLY HIS ASP ALA ILE ASN LEU SEQRES 10 A 198 GLU LEU HIS ALA THR ALA HIS ALA ILE ASP HIS ILE VAL SEQRES 11 A 198 LEU ASN ASP ILE SER LYS SER ALA GLN PHE LYS GLN ILE SEQRES 12 A 198 PHE ALA LYS GLU GLY ARG SER LEU GLY ASN VAL ASN PHE SEQRES 13 A 198 LEU GLY VAL TYR PRO GLU GLU PHE PHE ALA GLU SER PHE SEQRES 14 A 198 ALA TYR TYR TYR LEU ASN GLN ASP THR ASN SER LYS LEU SEQRES 15 A 198 LYS SER ALA CYS PRO GLN THR TYR SER PHE LEU GLN ASN SEQRES 16 A 198 LEU ALA LYS SEQRES 1 B 198 GLY SER HIS MET ASP SER THR THR ILE GLN GLN ASN LYS SEQRES 2 B 198 ASP THR LEU SER GLN ILE VAL VAL PHE PRO THR GLY ASN SEQRES 3 B 198 TYR ASP LYS ASN GLU ALA ASN ALA MET VAL ASN ARG LEU SEQRES 4 B 198 ALA ASN ILE ASP GLY LYS TYR LEU ASN ALA LEU LYS GLN SEQRES 5 B 198 ASN ASN LEU LYS ILE LYS LEU LEU SER GLY LYS LEU THR SEQRES 6 B 198 ASP GLU LYS GLU TYR ALA TYR LEU LYS GLY VAL VAL PRO SEQRES 7 B 198 LYS GLY TRP GLU GLY THR GLY LYS THR TRP ASP ASP VAL SEQRES 8 B 198 PRO GLY LEU GLY GLY SER THR VAL ALA LEU ARG ILE GLY SEQRES 9 B 198 PHE SER ASN LYS GLY LYS GLY HIS ASP ALA ILE ASN LEU SEQRES 10 B 198 GLU LEU HIS ALA THR ALA HIS ALA ILE ASP HIS ILE VAL SEQRES 11 B 198 LEU ASN ASP ILE SER LYS SER ALA GLN PHE LYS GLN ILE SEQRES 12 B 198 PHE ALA LYS GLU GLY ARG SER LEU GLY ASN VAL ASN PHE SEQRES 13 B 198 LEU GLY VAL TYR PRO GLU GLU PHE PHE ALA GLU SER PHE SEQRES 14 B 198 ALA TYR TYR TYR LEU ASN GLN ASP THR ASN SER LYS LEU SEQRES 15 B 198 LYS SER ALA CYS PRO GLN THR TYR SER PHE LEU GLN ASN SEQRES 16 B 198 LEU ALA LYS SEQRES 1 C 8 ACE GLU VAL ASN ALA PRO VAL LPD SEQRES 1 D 8 ACE GLU VAL ASN ALA PRO VAL LPD HET ACE C 0 6 HET LPD C 7 17 HET ACE D 0 6 HET LPD D 125 17 HET ZN A 301 1 HET ZN B 301 1 HETNAM ACE ACETYL GROUP HETNAM LPD L-PROLINAMIDE HETNAM ZN ZINC ION FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 LPD 2(C5 H10 N2 O) FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *446(H2 O) HELIX 1 AA1 ASP A 27 GLN A 40 1 14 HELIX 2 AA2 ASP A 50 ALA A 62 1 13 HELIX 3 AA3 ASP A 65 ASN A 75 1 11 HELIX 4 AA4 LYS A 85 LYS A 96 5 12 HELIX 5 AA5 THR A 109 VAL A 113 5 5 HELIX 6 AA6 ASN A 138 VAL A 152 1 15 HELIX 7 AA7 ASP A 155 LYS A 158 5 4 HELIX 8 AA8 SER A 159 GLY A 170 1 12 HELIX 9 AA9 TYR A 182 ASN A 197 1 16 HELIX 10 AB1 ASN A 197 CYS A 208 1 12 HELIX 11 AB2 CYS A 208 ALA A 219 1 12 HELIX 12 AB3 THR B 30 GLN B 40 1 11 HELIX 13 AB4 ASP B 50 ALA B 62 1 13 HELIX 14 AB5 ASP B 65 ASN B 75 1 11 HELIX 15 AB6 LYS B 85 LYS B 96 5 12 HELIX 16 AB7 THR B 109 VAL B 113 5 5 HELIX 17 AB8 ASN B 138 VAL B 152 1 15 HELIX 18 AB9 ASP B 155 LYS B 158 5 4 HELIX 19 AC1 SER B 159 GLY B 170 1 12 HELIX 20 AC2 TYR B 182 ASN B 197 1 16 HELIX 21 AC3 ASN B 197 CYS B 208 1 12 HELIX 22 AC4 CYS B 208 ALA B 219 1 12 SHEET 1 AA1 5 VAL A 42 VAL A 43 0 SHEET 2 AA1 5 ILE A 79 LEU A 82 1 O ILE A 79 N VAL A 43 SHEET 3 AA1 5 VAL A 121 ARG A 124 1 O LEU A 123 N LEU A 82 SHEET 4 AA1 5 GLY A 115 GLY A 118 -1 N LEU A 116 O ALA A 122 SHEET 5 AA1 5 VAL D 120 ASN D 121 -1 O ASN D 121 N GLY A 117 SHEET 1 AA2 5 VAL B 42 VAL B 43 0 SHEET 2 AA2 5 ILE B 79 LEU B 82 1 O LEU B 81 N VAL B 43 SHEET 3 AA2 5 VAL B 121 ARG B 124 1 O LEU B 123 N LEU B 82 SHEET 4 AA2 5 GLY B 115 GLY B 118 -1 N LEU B 116 O ALA B 122 SHEET 5 AA2 5 VAL C 2 ASN C 3 -1 O ASN C 3 N GLY B 117 LINK C ACE C 0 N GLU C 1 1555 1555 1.33 LINK C VAL C 6 N LPD C 7 1555 1555 1.32 LINK C ACE D 0 N GLU D 119 1555 1555 1.33 LINK C VAL D 124 N LPD D 125 1555 1555 1.33 LINK NE2 HIS A 142 ZN ZN A 301 1555 1555 2.02 LINK NE2 HIS A 146 ZN ZN A 301 1555 1555 2.36 LINK OE1 GLU A 185 ZN ZN A 301 1555 1555 1.89 LINK ZN ZN A 301 O ALA D 122 1555 1555 2.36 LINK NE2 HIS B 142 ZN ZN B 301 1555 1555 1.97 LINK NE2 HIS B 146 ZN ZN B 301 1555 1555 2.21 LINK OE1 GLU B 185 ZN ZN B 301 1555 1555 1.90 LINK ZN ZN B 301 O ALA C 4 1555 1555 2.44 SITE 1 AC1 4 HIS A 142 HIS A 146 GLU A 185 ALA D 122 SITE 1 AC2 4 HIS B 142 HIS B 146 GLU B 185 ALA C 4 SITE 1 AC3 7 GLY B 118 SER B 119 HIS B 150 VAL C 2 SITE 2 AC3 7 ASN C 3 HOH C 101 HOH C 102 SITE 1 AC4 12 GLU A 104 GLY A 105 GLY B 102 TRP B 103 SITE 2 AC4 12 HIS B 134 ASP B 135 ALA B 136 ASN B 175 SITE 3 AC4 12 PHE B 178 HOH B 409 HOH B 468 PRO C 5 SITE 1 AC5 6 GLY A 118 SER A 119 HIS A 150 GLN A 198 SITE 2 AC5 6 VAL D 120 HOH D 201 SITE 1 AC6 9 GLY A 102 HIS A 134 ASP A 135 ASN A 175 SITE 2 AC6 9 PHE A 178 HOH A 408 HOH A 501 PRO D 123 SITE 3 AC6 9 HOH D 204 CRYST1 37.364 42.923 123.354 90.00 96.28 90.00 P 1 21 1 4 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 0.026764 0.000000 0.002944 0.00000 SCALE2 0.000000 0.023298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008156 0.00000