HEADER HYDROLASE/PEPTIDE 10-JUL-13 4BXE TITLE CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX TITLE 2 WITH ANHYDROMURAMIC PENTAPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMPDH3; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANHYDROMURAMIC PEPTIDE; COMPND 7 CHAIN: C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET28; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.ARTOLA-RECOLONS,J.A.HERMOSO REVDAT 4 01-MAY-24 4BXE 1 REMARK REVDAT 3 15-NOV-23 4BXE 1 REMARK LINK ATOM REVDAT 2 16-OCT-13 4BXE 1 COMPND HETATM REVDAT 1 09-OCT-13 4BXE 0 JRNL AUTH M.LEE,C.ARTOLA-RECOLONS,C.CARRASCO-LOPEZ, JRNL AUTH 2 S.MARTINEZ-CABALLERO,D.HESEK,E.SPINK,E.LASTOCHKIN,W.ZHANG, JRNL AUTH 3 L.M.HELLMAN,B.BOGGESS,J.A.HERMOSO,S.MOBASHERY JRNL TITL CELL-WALL REMODELING BY THE ZINC-PROTEASE AMPDH3 FROM JRNL TITL 2 PSEUDOMONAS AERUGINOSA. JRNL REF J.AM.CHEM.SOC. V. 135 12604 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23931161 JRNL DOI 10.1021/JA407445X REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18648 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 951 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 48.2754 - 5.6406 1.00 2729 118 0.1873 0.2362 REMARK 3 2 5.6406 - 4.4781 1.00 2566 128 0.1615 0.2138 REMARK 3 3 4.4781 - 3.9124 1.00 2503 155 0.1554 0.2248 REMARK 3 4 3.9124 - 3.5548 1.00 2492 137 0.1816 0.2363 REMARK 3 5 3.5548 - 3.3000 1.00 2477 137 0.2421 0.3117 REMARK 3 6 3.3000 - 3.1055 1.00 2457 146 0.2846 0.3673 REMARK 3 7 3.1055 - 2.9500 1.00 2473 130 0.3442 0.4155 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) : 0.530 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.56 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 : 0.009 4317 REMARK 3 ANGLE : 1.491 5869 REMARK 3 CHIRALITY : 0.091 620 REMARK 3 PLANARITY : 0.005 773 REMARK 3 DIHEDRAL : 17.325 1542 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 1 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.8917 5.3512 9.1793 REMARK 3 T TENSOR REMARK 3 T11: 0.3408 T22: 0.3839 REMARK 3 T33: 0.2533 T12: -0.1426 REMARK 3 T13: -0.0377 T23: 0.0484 REMARK 3 L TENSOR REMARK 3 L11: 1.5035 L22: 1.6215 REMARK 3 L33: 0.7489 L12: 0.4564 REMARK 3 L13: -0.8745 L23: -0.4796 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: 0.1780 S13: -0.0844 REMARK 3 S21: 0.1878 S22: 0.0652 S23: 0.1249 REMARK 3 S31: 0.1072 S32: -0.3293 S33: -0.0772 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 95 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.9339 1.0071 22.2090 REMARK 3 T TENSOR REMARK 3 T11: 0.6071 T22: 0.5135 REMARK 3 T33: 0.4629 T12: -0.1171 REMARK 3 T13: 0.0450 T23: 0.1596 REMARK 3 L TENSOR REMARK 3 L11: 0.2404 L22: 1.3449 REMARK 3 L33: 1.9570 L12: 0.6727 REMARK 3 L13: -0.1463 L23: -0.2279 REMARK 3 S TENSOR REMARK 3 S11: 0.0207 S12: -0.4253 S13: 0.0217 REMARK 3 S21: 0.5445 S22: 0.1712 S23: 0.4218 REMARK 3 S31: 0.3492 S32: -0.3918 S33: -0.0344 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 135 THROUGH 255 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1213 18.2225 30.2704 REMARK 3 T TENSOR REMARK 3 T11: 0.5522 T22: 0.4259 REMARK 3 T33: 0.2957 T12: -0.1047 REMARK 3 T13: 0.1022 T23: 0.0721 REMARK 3 L TENSOR REMARK 3 L11: 2.1346 L22: 0.7826 REMARK 3 L33: 1.6744 L12: -0.1676 REMARK 3 L13: -0.4014 L23: 0.6374 REMARK 3 S TENSOR REMARK 3 S11: 0.1207 S12: -0.1830 S13: 0.1521 REMARK 3 S21: 0.4003 S22: -0.0131 S23: 0.1439 REMARK 3 S31: -0.0259 S32: -0.2200 S33: -0.0957 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND (RESID 1 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.0320 20.5547 -3.5736 REMARK 3 T TENSOR REMARK 3 T11: 0.2245 T22: 0.3601 REMARK 3 T33: 0.2250 T12: -0.0743 REMARK 3 T13: -0.0629 T23: 0.0479 REMARK 3 L TENSOR REMARK 3 L11: 0.7725 L22: 1.2899 REMARK 3 L33: 0.9068 L12: -0.3273 REMARK 3 L13: -0.4211 L23: 0.1116 REMARK 3 S TENSOR REMARK 3 S11: 0.1275 S12: 0.0857 S13: 0.0816 REMARK 3 S21: 0.1502 S22: 0.0323 S23: 0.0166 REMARK 3 S31: -0.1321 S32: -0.0086 S33: -0.0202 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN B AND (RESID 101 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.4640 41.1544 -12.4317 REMARK 3 T TENSOR REMARK 3 T11: 0.5913 T22: 0.5027 REMARK 3 T33: 0.6837 T12: -0.0057 REMARK 3 T13: 0.0784 T23: 0.1111 REMARK 3 L TENSOR REMARK 3 L11: 1.5398 L22: 1.5204 REMARK 3 L33: 0.2451 L12: -0.5503 REMARK 3 L13: 0.5265 L23: -0.5600 REMARK 3 S TENSOR REMARK 3 S11: -0.1260 S12: 0.4362 S13: 0.8780 REMARK 3 S21: 0.0228 S22: 0.2719 S23: 0.4512 REMARK 3 S31: -1.1335 S32: 0.1003 S33: 0.0191 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN B AND (RESID 118 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.4393 24.9042 -13.2893 REMARK 3 T TENSOR REMARK 3 T11: 0.2821 T22: 0.4216 REMARK 3 T33: 0.2493 T12: 0.0045 REMARK 3 T13: -0.0303 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 1.4817 L22: 0.8981 REMARK 3 L33: 0.7793 L12: -0.2155 REMARK 3 L13: 0.1557 L23: -0.6058 REMARK 3 S TENSOR REMARK 3 S11: 0.0948 S12: 0.2353 S13: -0.0256 REMARK 3 S21: -0.0085 S22: -0.0475 S23: -0.0356 REMARK 3 S31: -0.1259 S32: -0.1689 S33: -0.0125 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN B AND (RESID 177 THROUGH 255 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.4013 35.4682 -10.4040 REMARK 3 T TENSOR REMARK 3 T11: 0.3070 T22: 0.4722 REMARK 3 T33: 0.2545 T12: -0.0088 REMARK 3 T13: -0.0196 T23: 0.0674 REMARK 3 L TENSOR REMARK 3 L11: 1.7934 L22: 2.0301 REMARK 3 L33: 1.0479 L12: -0.7098 REMARK 3 L13: 0.0178 L23: 0.5767 REMARK 3 S TENSOR REMARK 3 S11: -0.0173 S12: -0.1180 S13: 0.0611 REMARK 3 S21: 0.0136 S22: 0.0100 S23: 0.0651 REMARK 3 S31: -0.0976 S32: -0.2275 S33: 0.0354 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 4BXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1290057613. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 8 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87290 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18710 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 48.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.82000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: IMOSFLM, SCALA, MOLREP, PHENIX REMARK 200 STARTING MODEL: AMPDH3-NATIVE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.62500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.47000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.47000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.31250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.47000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.47000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 123.93750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.47000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.47000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.31250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.47000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.47000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 123.93750 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 82.62500 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 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 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS B 146 NE2 HIS B 146 CD2 -0.067 REMARK 500 ALA D 2 C DGL D 3 N 0.168 REMARK 500 DGL D 3 CD DGL D 3 OE1 -0.073 REMARK 500 DGL D 3 CD DGL D 3 OE2 3.774 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 AH0 C 1 CA - C - N ANGL. DEV. = 14.6 DEGREES REMARK 500 ALA C 2 N - CA - C ANGL. DEV. = -18.8 DEGREES REMARK 500 ALA C 2 CA - C - O ANGL. DEV. = -12.6 DEGREES REMARK 500 ALA C 2 CA - C - N ANGL. DEV. = 13.4 DEGREES REMARK 500 DAL C 6 CB - CA - C ANGL. DEV. = -9.8 DEGREES REMARK 500 AH0 D 1 CA - C - N ANGL. DEV. = 15.7 DEGREES REMARK 500 AH0 D 1 O - C - N ANGL. DEV. = -11.9 DEGREES REMARK 500 ALA D 2 N - CA - C ANGL. DEV. = -16.8 DEGREES REMARK 500 ALA D 2 CA - C - N ANGL. DEV. = 13.5 DEGREES REMARK 500 DGL D 3 OE1 - CD - OE2 ANGL. DEV. = -20.7 DEGREES REMARK 500 DGL D 3 CG - CD - OE2 ANGL. DEV. = -66.7 DEGREES REMARK 500 DGL D 3 CA - C - O ANGL. DEV. = -14.4 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 THR A 12 -80.47 -116.51 REMARK 500 ALA A 28 18.00 80.95 REMARK 500 ALA A 37 -70.94 -60.86 REMARK 500 ALA A 59 2.85 -68.91 REMARK 500 LYS A 63 -69.68 -105.13 REMARK 500 TRP A 78 77.94 -104.73 REMARK 500 TRP A 85 140.08 -171.81 REMARK 500 ASN A 102 127.98 -170.52 REMARK 500 ASP A 106 -37.43 -136.27 REMARK 500 ASP A 107 31.29 -90.92 REMARK 500 PRO A 210 -179.13 -65.63 REMARK 500 ARG A 230 54.71 -151.43 REMARK 500 THR B 12 -80.96 -103.31 REMARK 500 LYS B 63 -66.68 -139.97 REMARK 500 ALA B 72 157.25 -42.85 REMARK 500 TRP B 78 74.92 -102.08 REMARK 500 ALA B 86 -126.52 45.17 REMARK 500 ASP B 89 11.57 -150.83 REMARK 500 THR B 94 11.85 -142.85 REMARK 500 ALA B 150 65.62 -113.32 REMARK 500 ASN B 233 105.20 -161.61 REMARK 500 TYR B 253 66.92 -117.06 REMARK 500 ALA C 2 -171.29 128.41 REMARK 500 ALA D 2 -130.59 -165.49 REMARK 500 DAL D 5 -179.02 -89.48 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 ASP B 93 THR B 94 -148.46 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 A2001 DISTANCE = 5.91 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1263 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1264 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 1266 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 1267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF PEPTIDE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF PEPTIDE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BXD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX REMARK 900 WITH TETRASACCHARIDE PENTAPEPTIDE REMARK 900 RELATED ID: 4BXJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA DBREF 4BXE A 1 255 UNP Q9I5D1 Q9I5D1_PSEAE 1 255 DBREF 4BXE B 1 255 UNP Q9I5D1 Q9I5D1_PSEAE 1 255 DBREF 4BXE C 1 6 PDB 4BXE 4BXE 1 6 DBREF 4BXE D 1 6 PDB 4BXE 4BXE 1 6 SEQRES 1 A 255 MET LEU THR ILE ASP TYR ASN SER TYR ARG THR THR THR SEQRES 2 A 255 PRO TYR GLY LYS ARG VAL ARG PHE LEU VAL LEU HIS TYR SEQRES 3 A 255 THR ALA LEU ASP PHE ALA ALA SER VAL LYS ALA LEU THR SEQRES 4 A 255 THR GLY ALA ALA SER ALA HIS TYR LEU ILE PRO ALA PRO SEQRES 5 A 255 HIS ASP PRO SER TYR LYS ALA ALA GLY PHE LYS GLY GLN SEQRES 6 A 255 ARG ILE PHE ASN LEU VAL ALA GLU GLU ASP ARG ALA TRP SEQRES 7 A 255 HIS ALA GLY VAL SER GLY TRP ALA ARG ARG ASP ASN LEU SEQRES 8 A 255 ASN ASP THR SER ILE GLY ILE GLU ILE VAL ASN LEU ALA SEQRES 9 A 255 ARG ASP ASP ASP GLY VAL PHE THR PHE PRO ASP TYR GLU SEQRES 10 A 255 ARG SER GLN ILE ASN ALA LEU LYS GLN LEU ALA LYS ASN SEQRES 11 A 255 ILE LEU GLN ARG TYR PRO ASP MET THR PRO LYS ASN VAL SEQRES 12 A 255 VAL GLY HIS SER ASP ILE ALA VAL GLY ARG LYS SER ASP SEQRES 13 A 255 PRO GLY PRO LYS LEU PRO TRP LYS GLU LEU TYR GLU ALA SEQRES 14 A 255 GLY ILE GLY ALA TRP TYR ASP ASP ALA THR ARG ASP ARG SEQRES 15 A 255 TYR ARG GLU GLY PHE GLU ARG ASP GLY LEU PRO PRO ARG SEQRES 16 A 255 ALA ASP LEU LEU GLU ALA PHE ARG LEU TYR GLY TYR ALA SEQRES 17 A 255 LEU PRO ALA THR VAL ASP ASP ALA TYR PHE ALA SER LEU SEQRES 18 A 255 LEU ARG ALA PHE GLN MET HIS PHE ARG PRO GLU ASN TYR SEQRES 19 A 255 ASP GLY ALA LEU ASP VAL GLU THR ALA ALA ILE LEU TYR SEQRES 20 A 255 ALA LEU ASN GLU LYS TYR PRO ALA SEQRES 1 B 255 MET LEU THR ILE ASP TYR ASN SER TYR ARG THR THR THR SEQRES 2 B 255 PRO TYR GLY LYS ARG VAL ARG PHE LEU VAL LEU HIS TYR SEQRES 3 B 255 THR ALA LEU ASP PHE ALA ALA SER VAL LYS ALA LEU THR SEQRES 4 B 255 THR GLY ALA ALA SER ALA HIS TYR LEU ILE PRO ALA PRO SEQRES 5 B 255 HIS ASP PRO SER TYR LYS ALA ALA GLY PHE LYS GLY GLN SEQRES 6 B 255 ARG ILE PHE ASN LEU VAL ALA GLU GLU ASP ARG ALA TRP SEQRES 7 B 255 HIS ALA GLY VAL SER GLY TRP ALA ARG ARG ASP ASN LEU SEQRES 8 B 255 ASN ASP THR SER ILE GLY ILE GLU ILE VAL ASN LEU ALA SEQRES 9 B 255 ARG ASP ASP ASP GLY VAL PHE THR PHE PRO ASP TYR GLU SEQRES 10 B 255 ARG SER GLN ILE ASN ALA LEU LYS GLN LEU ALA LYS ASN SEQRES 11 B 255 ILE LEU GLN ARG TYR PRO ASP MET THR PRO LYS ASN VAL SEQRES 12 B 255 VAL GLY HIS SER ASP ILE ALA VAL GLY ARG LYS SER ASP SEQRES 13 B 255 PRO GLY PRO LYS LEU PRO TRP LYS GLU LEU TYR GLU ALA SEQRES 14 B 255 GLY ILE GLY ALA TRP TYR ASP ASP ALA THR ARG ASP ARG SEQRES 15 B 255 TYR ARG GLU GLY PHE GLU ARG ASP GLY LEU PRO PRO ARG SEQRES 16 B 255 ALA ASP LEU LEU GLU ALA PHE ARG LEU TYR GLY TYR ALA SEQRES 17 B 255 LEU PRO ALA THR VAL ASP ASP ALA TYR PHE ALA SER LEU SEQRES 18 B 255 LEU ARG ALA PHE GLN MET HIS PHE ARG PRO GLU ASN TYR SEQRES 19 B 255 ASP GLY ALA LEU ASP VAL GLU THR ALA ALA ILE LEU TYR SEQRES 20 B 255 ALA LEU ASN GLU LYS TYR PRO ALA SEQRES 1 C 6 AH0 ALA DGL API DAL DAL SEQRES 1 D 6 AH0 ALA DGL API DAL DAL MODRES 4BXE API C 4 LYS 2,6-DIAMINOPIMELIC ACID MODRES 4BXE API D 4 LYS 2,6-DIAMINOPIMELIC ACID HET AH0 C 1 18 HET DGL C 3 9 HET API C 4 12 HET DAL C 5 5 HET DAL C 6 6 HET AH0 D 1 18 HET DGL D 3 9 HET API D 4 12 HET DAL D 5 5 HET DAL D 6 6 HET ACT A1263 4 HET ACT B1264 4 HET ACT B1265 4 HET PEG B1266 7 HET PEG B1267 7 HETNAM AH0 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT- HETNAM 2 AH0 3-YLOXY)-PROPIONIC ACID HETNAM DGL D-GLUTAMIC ACID HETNAM API 2,6-DIAMINOPIMELIC ACID HETNAM DAL D-ALANINE HETNAM ACT ACETATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN AH0 1,6-ANHYDRO-N-ACETYLMURAMIC ACID FORMUL 3 AH0 2(C11 H17 N O7) FORMUL 3 DGL 2(C5 H9 N O4) FORMUL 3 API 2(C7 H14 N2 O4) FORMUL 3 DAL 4(C3 H7 N O2) FORMUL 5 ACT 3(C2 H3 O2 1-) FORMUL 8 PEG 2(C4 H10 O3) FORMUL 10 HOH *73(H2 O) HELIX 1 1 ASP A 30 GLY A 41 1 12 HELIX 2 2 ASP A 54 ALA A 59 1 6 HELIX 3 3 GLU A 117 GLN A 133 1 17 HELIX 4 4 THR A 139 LYS A 141 5 3 HELIX 5 5 HIS A 146 ALA A 150 1 5 HELIX 6 6 PRO A 162 ALA A 169 1 8 HELIX 7 7 ASP A 176 GLY A 191 1 16 HELIX 8 8 PRO A 194 GLY A 206 1 13 HELIX 9 9 ASP A 214 ARG A 230 1 17 HELIX 10 10 ASP A 239 TYR A 253 1 15 HELIX 11 11 ASP B 30 GLY B 41 1 12 HELIX 12 12 ASP B 54 ALA B 59 1 6 HELIX 13 13 ASN B 90 ASP B 93 5 4 HELIX 14 14 GLU B 117 GLN B 133 1 17 HELIX 15 15 THR B 139 LYS B 141 5 3 HELIX 16 16 HIS B 146 ALA B 150 1 5 HELIX 17 17 PRO B 162 ALA B 169 1 8 HELIX 18 18 ASP B 176 GLY B 191 1 16 HELIX 19 19 PRO B 194 GLY B 206 1 13 HELIX 20 20 ASP B 214 ARG B 230 1 17 HELIX 21 21 ASP B 239 TYR B 253 1 15 SHEET 1 AA 2 TYR A 15 LYS A 17 0 SHEET 2 AA 2 ASP B 75 ALA B 77 -1 O ARG B 76 N GLY A 16 SHEET 1 AB 5 PHE A 68 ASN A 69 0 SHEET 2 AB 5 TYR A 47 ILE A 49 -1 O LEU A 48 N PHE A 68 SHEET 3 AB 5 SER A 95 ILE A 100 1 O GLY A 97 N TYR A 47 SHEET 4 AB 5 PHE A 21 TYR A 26 1 O PHE A 21 N ILE A 96 SHEET 5 AB 5 VAL A 143 GLY A 145 1 O VAL A 144 N LEU A 24 SHEET 1 AC 2 ASP A 75 ALA A 77 0 SHEET 2 AC 2 TYR B 15 LYS B 17 -1 O GLY B 16 N ARG A 76 SHEET 1 BA 5 PHE B 68 ASN B 69 0 SHEET 2 BA 5 TYR B 47 ILE B 49 -1 O LEU B 48 N PHE B 68 SHEET 3 BA 5 SER B 95 ILE B 100 1 O GLY B 97 N TYR B 47 SHEET 4 BA 5 PHE B 21 TYR B 26 1 O PHE B 21 N ILE B 96 SHEET 5 BA 5 VAL B 143 GLY B 145 1 O VAL B 144 N LEU B 24 LINK C AH0 C 1 N ALA C 2 1555 1555 1.46 LINK C ALA C 2 N DGL C 3 1555 1555 1.47 LINK CD DGL C 3 N API C 4 1555 1555 1.43 LINK C API C 4 N DAL C 5 1555 1555 1.41 LINK C DAL C 5 N DAL C 6 1555 1555 1.47 LINK C AH0 D 1 N ALA D 2 1555 1555 1.45 LINK C ALA D 2 N DGL D 3 1555 1555 1.50 LINK CD DGL D 3 N API D 4 1555 1555 1.43 LINK C API D 4 N DAL D 5 1555 1555 1.41 LINK C DAL D 5 N DAL D 6 1555 1555 1.45 CISPEP 1 MET A 1 LEU A 2 0 1.96 CISPEP 2 ASP A 156 PRO A 157 0 0.60 CISPEP 3 ASP B 108 GLY B 109 0 -1.78 CISPEP 4 ASP B 156 PRO B 157 0 5.86 CISPEP 5 AH0 C 1 ALA C 2 0 0.04 CISPEP 6 ALA C 2 DGL C 3 0 0.67 CISPEP 7 AH0 D 1 ALA D 2 0 -0.61 CISPEP 8 ALA D 2 DGL D 3 0 -5.76 SITE 1 AC1 2 ASP B 181 HOH B2044 SITE 1 AC2 3 SER B 8 TYR B 9 HOH B2041 SITE 1 AC3 2 ASN B 233 TYR B 234 SITE 1 AC4 3 TYR A 6 ARG A 134 ARG B 134 SITE 1 AC5 3 HIS B 53 LYS B 63 GLY B 64 SITE 1 AC6 16 THR A 27 ALA A 28 ARG A 76 TRP A 78 SITE 2 AC6 16 HIS A 79 ALA A 80 GLY A 81 ASN A 90 SITE 3 AC6 16 ASN A 92 GLU A 99 HIS A 146 ARG A 153 SITE 4 AC6 16 LYS A 154 ASP A 156 ARG B 20 ASP B 137 SITE 1 AC7 23 ARG A 20 ARG A 88 ASP A 137 HOH A2017 SITE 2 AC7 23 TYR B 26 THR B 27 ALA B 28 LEU B 29 SITE 3 AC7 23 ALA B 43 ARG B 76 TRP B 78 HIS B 79 SITE 4 AC7 23 ALA B 80 GLY B 81 ASN B 92 GLU B 99 SITE 5 AC7 23 HIS B 146 ARG B 153 LYS B 154 ASP B 156 SITE 6 AC7 23 HOH B2008 HOH B2039 HOH B2040 CRYST1 100.940 100.940 165.250 90.00 90.00 90.00 P 41 21 2 16 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 0.009907 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006051 0.00000