HEADER HYDROLASE/PEPTIDE 10-JUL-13 4BXD TITLE CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX TITLE 2 WITH TETRASACCHARIDE 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: 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 4BXD 1 HETSYN LINK REVDAT 3 29-JUL-20 4BXD 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 16-OCT-13 4BXD 1 ATOM ANISOU HETATM REVDAT 1 09-OCT-13 4BXD 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. 3.10 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 15149 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 759 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 48.3055 - 5.2991 0.98 3152 159 0.1860 0.2380 REMARK 3 2 5.2991 - 4.2068 0.98 2949 164 0.1761 0.2071 REMARK 3 3 4.2068 - 3.6753 0.96 2876 141 0.2139 0.2826 REMARK 3 4 3.6753 - 3.3393 0.93 2724 161 0.2784 0.3763 REMARK 3 5 3.3393 - 3.1000 0.91 2689 134 0.3558 0.3673 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.43 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 : 0.023 4335 REMARK 3 ANGLE : 1.899 5904 REMARK 3 CHIRALITY : 0.090 636 REMARK 3 PLANARITY : 0.007 769 REMARK 3 DIHEDRAL : 16.662 1532 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 1 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7835 -19.6098 45.6659 REMARK 3 T TENSOR REMARK 3 T11: 0.1923 T22: 0.1838 REMARK 3 T33: 0.3415 T12: 0.0602 REMARK 3 T13: -0.0135 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 2.0961 L22: 1.6035 REMARK 3 L33: 2.5689 L12: -0.1006 REMARK 3 L13: 0.2911 L23: -1.5485 REMARK 3 S TENSOR REMARK 3 S11: -0.0458 S12: -0.2440 S13: -0.2226 REMARK 3 S21: -0.0699 S22: 0.0718 S23: -0.1661 REMARK 3 S31: -0.0404 S32: -0.1001 S33: -0.0568 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 67 THROUGH 84 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9151 -22.3623 41.6670 REMARK 3 T TENSOR REMARK 3 T11: 0.1337 T22: 0.3061 REMARK 3 T33: 0.5866 T12: 0.2092 REMARK 3 T13: 0.1167 T23: 0.0906 REMARK 3 L TENSOR REMARK 3 L11: 0.8202 L22: 0.7026 REMARK 3 L33: 2.8233 L12: 0.5037 REMARK 3 L13: 1.4669 L23: 0.6660 REMARK 3 S TENSOR REMARK 3 S11: -0.1923 S12: -0.1568 S13: 0.8069 REMARK 3 S21: 0.0087 S22: -0.3268 S23: -0.0588 REMARK 3 S31: -0.0854 S32: -0.4150 S33: 0.3373 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 85 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.3713 -29.2335 50.8458 REMARK 3 T TENSOR REMARK 3 T11: 0.2098 T22: 0.3477 REMARK 3 T33: 0.3916 T12: 0.0539 REMARK 3 T13: -0.0305 T23: 0.0494 REMARK 3 L TENSOR REMARK 3 L11: 2.3003 L22: 2.6523 REMARK 3 L33: 3.6674 L12: 2.3913 REMARK 3 L13: -0.1826 L23: -0.1889 REMARK 3 S TENSOR REMARK 3 S11: 0.1011 S12: -0.1691 S13: -0.3794 REMARK 3 S21: 0.0307 S22: -0.0297 S23: -0.4139 REMARK 3 S31: 0.4495 S32: -0.1545 S33: -0.1145 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 133 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.0263 -28.2302 54.4927 REMARK 3 T TENSOR REMARK 3 T11: 0.1451 T22: 0.4092 REMARK 3 T33: 0.3432 T12: 0.0237 REMARK 3 T13: 0.0584 T23: 0.0608 REMARK 3 L TENSOR REMARK 3 L11: 2.8307 L22: 2.4366 REMARK 3 L33: 1.1585 L12: 1.3795 REMARK 3 L13: -0.6003 L23: 0.0485 REMARK 3 S TENSOR REMARK 3 S11: 0.1399 S12: -0.3252 S13: 0.0744 REMARK 3 S21: 0.0871 S22: 0.1159 S23: 0.1988 REMARK 3 S31: 0.0439 S32: -0.4956 S33: -0.2022 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND (RESID 190 THROUGH 229 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.0857 -36.6977 45.3577 REMARK 3 T TENSOR REMARK 3 T11: 0.2008 T22: 0.1881 REMARK 3 T33: 0.2550 T12: 0.0519 REMARK 3 T13: 0.0710 T23: 0.0325 REMARK 3 L TENSOR REMARK 3 L11: 7.1349 L22: 5.3276 REMARK 3 L33: 6.0910 L12: 4.2216 REMARK 3 L13: 2.2867 L23: 1.5117 REMARK 3 S TENSOR REMARK 3 S11: -0.1474 S12: 0.4273 S13: 0.0127 REMARK 3 S21: -0.2723 S22: 0.1373 S23: -0.0834 REMARK 3 S31: 0.4965 S32: 0.0819 S33: -0.1229 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND (RESID 230 THROUGH 255 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.0355 -34.1811 54.5221 REMARK 3 T TENSOR REMARK 3 T11: 0.2477 T22: 0.4911 REMARK 3 T33: 0.2305 T12: 0.0213 REMARK 3 T13: 0.0601 T23: 0.1372 REMARK 3 L TENSOR REMARK 3 L11: 8.1536 L22: 6.2573 REMARK 3 L33: 4.1133 L12: -1.4759 REMARK 3 L13: 0.1367 L23: 4.9347 REMARK 3 S TENSOR REMARK 3 S11: -0.0374 S12: -0.8538 S13: -0.2525 REMARK 3 S21: 0.5911 S22: 0.0484 S23: 0.3284 REMARK 3 S31: 0.0888 S32: -0.3550 S33: -0.0487 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN B AND (RESID 1 THROUGH 84 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.7762 -4.2148 31.8930 REMARK 3 T TENSOR REMARK 3 T11: 0.2276 T22: 0.2737 REMARK 3 T33: 0.4131 T12: 0.0299 REMARK 3 T13: 0.0278 T23: 0.0597 REMARK 3 L TENSOR REMARK 3 L11: 0.7082 L22: 1.4850 REMARK 3 L33: 2.0611 L12: -0.3587 REMARK 3 L13: 0.4591 L23: -0.7450 REMARK 3 S TENSOR REMARK 3 S11: -0.0383 S12: 0.0425 S13: 0.2916 REMARK 3 S21: -0.1158 S22: -0.1176 S23: -0.1029 REMARK 3 S31: -0.2482 S32: -0.2316 S33: 0.1345 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN B AND (RESID 85 THROUGH 255 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.2135 -15.1245 13.8034 REMARK 3 T TENSOR REMARK 3 T11: 0.3074 T22: 0.3582 REMARK 3 T33: 0.3028 T12: 0.1107 REMARK 3 T13: -0.0732 T23: 0.0613 REMARK 3 L TENSOR REMARK 3 L11: 2.3559 L22: 3.1922 REMARK 3 L33: 3.0084 L12: 1.1961 REMARK 3 L13: 0.4016 L23: 1.3415 REMARK 3 S TENSOR REMARK 3 S11: -0.0662 S12: 0.2685 S13: 0.0441 REMARK 3 S21: -0.5665 S22: -0.0102 S23: 0.4459 REMARK 3 S31: -0.2217 S32: -0.6070 S33: 0.0544 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 4BXD 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_1290057615. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 10 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97166 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15988 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 48.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.600 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 (%): 65.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 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 81.13050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.59300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.59300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.56525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.59300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.59300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 121.69575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.59300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.59300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 40.56525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.59300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.59300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 121.69575 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 81.13050 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 HD1 HIS B 25 ZN ZN B 1256 1.07 REMARK 500 OD2 ASP A 93 HH21 ARG B 88 1.23 REMARK 500 OE1 GLU B 73 HH TYR B 135 1.24 REMARK 500 HH11 ARG B 76 OD1 ASP B 93 1.45 REMARK 500 O ASP B 235 H ALA B 237 1.48 REMARK 500 O VAL B 35 HG1 THR B 39 1.48 REMARK 500 HH21 ARG A 18 O GLU B 73 1.51 REMARK 500 O SER A 95 HH22 ARG B 18 1.52 REMARK 500 O ARG B 118 H ILE B 121 1.55 REMARK 500 HD1 HIS A 146 OD2 ASP A 156 1.57 REMARK 500 H1 ALA C 1 O HOH A 2005 1.58 REMARK 500 O TRP B 163 H LEU B 166 1.58 REMARK 500 H2 ALA C 1 O HOH A 2005 1.58 REMARK 500 H2 ALA D 1 O HOH B 2008 1.58 REMARK 500 H1 ALA D 1 O HOH B 2008 1.58 REMARK 500 HH12 ARG A 76 O 6CL C 3 1.59 REMARK 500 HZ2 LYS B 154 O3 MAG F 1 1.59 REMARK 500 O ILE B 131 H ARG B 134 1.60 REMARK 500 N ALA D 1 O HOH B 2008 1.89 REMARK 500 N ALA C 1 O HOH A 2005 1.89 REMARK 500 NZ LYS B 154 O3 MAG F 1 1.94 REMARK 500 OD2 ASP A 5 OG SER A 8 1.96 REMARK 500 OE1 GLU B 73 OH TYR B 135 2.02 REMARK 500 OD2 ASP A 93 NH2 ARG B 88 2.03 REMARK 500 OD2 ASP B 5 OG SER B 8 2.08 REMARK 500 O ALA B 80 OG SER B 83 2.10 REMARK 500 NH2 ARG B 230 OD2 ASP B 239 2.14 REMARK 500 O3 NAG F 2 O7 NAG F 3 2.16 REMARK 500 NH1 ARG B 230 OD1 ASN B 233 2.16 REMARK 500 O TRP B 163 N LEU B 166 2.17 REMARK 500 O ALA A 77 OD1 ASN A 92 2.18 REMARK 500 O ARG B 118 N ILE B 121 2.18 REMARK 500 O4 NAG F 2 O5 NAG F 3 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 26 CE1 TYR A 26 CZ -0.081 REMARK 500 HIS A 46 NE2 HIS A 46 CD2 -0.069 REMARK 500 HIS A 79 NE2 HIS A 79 CD2 -0.072 REMARK 500 PHE A 218 C ALA A 219 N 0.148 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 PRO B 140 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 6CL C 3 CA - C - N ANGL. DEV. = 19.3 DEGREES REMARK 500 6CL C 3 O - C - N ANGL. DEV. = -10.9 DEGREES REMARK 500 6CL D 3 CA - C - N ANGL. DEV. = 16.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 12 -78.11 -99.96 REMARK 500 PRO A 14 42.09 -81.90 REMARK 500 ALA A 28 17.62 81.33 REMARK 500 ASP A 30 -172.55 -66.38 REMARK 500 LYS A 63 -67.12 -138.02 REMARK 500 VAL A 82 98.72 -68.90 REMARK 500 TRP A 85 125.45 -172.53 REMARK 500 ALA A 86 60.07 63.62 REMARK 500 ARG A 87 17.96 54.99 REMARK 500 ASP A 89 -169.84 -126.64 REMARK 500 ASN A 90 64.55 37.51 REMARK 500 ASP A 115 153.56 -47.80 REMARK 500 PRO A 136 1.07 -55.60 REMARK 500 ALA A 150 57.14 -98.21 REMARK 500 ASP A 177 -36.17 -37.81 REMARK 500 TYR A 207 108.76 -55.23 REMARK 500 ARG A 230 65.22 -152.01 REMARK 500 TYR A 253 78.84 -115.23 REMARK 500 THR B 12 -77.70 -118.41 REMARK 500 ARG B 20 -38.30 -130.31 REMARK 500 ALA B 28 16.66 85.32 REMARK 500 THR B 40 -1.56 -140.18 REMARK 500 HIS B 53 65.25 -102.44 REMARK 500 ALA B 60 -8.85 -57.23 REMARK 500 ASN B 102 119.67 -167.00 REMARK 500 THR B 112 98.88 -162.18 REMARK 500 PRO B 140 -34.90 -38.34 REMARK 500 ALA B 150 70.57 -118.99 REMARK 500 PRO B 162 60.23 -61.34 REMARK 500 LYS B 164 -38.10 -38.06 REMARK 500 ARG B 189 -72.14 -58.77 REMARK 500 ARG B 230 52.39 -155.95 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 -149.59 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 A1260 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 25 ND1 REMARK 620 2 HIS A 146 ND1 83.0 REMARK 620 3 ASP A 156 OD2 112.0 64.4 REMARK 620 4 HOH A2005 O 147.9 128.4 90.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1256 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 25 ND1 REMARK 620 2 HIS B 146 ND1 77.8 REMARK 620 3 ASP B 156 OD2 113.3 123.2 REMARK 620 4 HOH B2008 O 138.0 129.3 80.5 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BXE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX REMARK 900 WITH ANHYDROMURAMIC PENTAPEPTIDE REMARK 900 RELATED ID: 4BXJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AMPDH3 FROM PSEUDOMONAS AERUGINOSA DBREF 4BXD A 1 255 UNP Q9I5D1 Q9I5D1_PSEAE 1 255 DBREF 4BXD B 1 255 UNP Q9I5D1 Q9I5D1_PSEAE 1 255 DBREF 4BXD C 1 4 PDB 4BXD 4BXD 1 4 DBREF 4BXD D 1 4 PDB 4BXD 4BXD 1 4 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 4 ALA FGA 6CL DAL SEQRES 1 D 4 ALA FGA 6CL DAL MODRES 4BXD 6CL C 3 LYS 6-CARBOXYLYSINE MODRES 4BXD 6CL D 3 LYS 6-CARBOXYLYSINE HET FGA C 2 15 HET 6CL C 3 23 HET DAL C 4 11 HET FGA D 2 15 HET 6CL D 3 23 HET DAL D 4 11 HET MAG E 1 32 HET NAG E 2 27 HET NAG E 3 28 HET MAG F 1 32 HET NAG F 2 27 HET NAG F 3 28 HET ZN A1260 1 HET ZN B1256 1 HETNAM FGA GAMMA-D-GLUTAMIC ACID HETNAM 6CL 6-CARBOXYLYSINE HETNAM DAL D-ALANINE HETNAM MAG METHYL 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSIDE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ZN ZINC ION HETSYN FGA D-GLUTAMIC ACID HETSYN MAG BETA-METHYL-N-ACETYL-D-GLUCOSAMINE; METHYL 2-ACETAMIDO- HETSYN 2 MAG 2-DEOXY-BETA-D-GLUCOSIDE; METHYL 2-ACETAMIDO-2-DEOXY- HETSYN 3 MAG D-GLUCOSIDE; METHYL 2-ACETAMIDO-2-DEOXY-GLUCOSIDE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 FGA 2(C5 H9 N O4) FORMUL 3 6CL 2(C7 H15 N2 O4 1+) FORMUL 3 DAL 2(C3 H7 N O2) FORMUL 5 MAG 2(C9 H17 N O6) FORMUL 5 NAG 4(C8 H15 N O6) FORMUL 7 ZN 2(ZN 2+) FORMUL 9 HOH *38(H2 O) HELIX 1 1 ASP A 30 THR A 40 1 11 HELIX 2 2 ASP A 54 ALA A 60 1 7 HELIX 3 3 ASN A 90 ASP A 93 5 4 HELIX 4 4 GLU A 117 GLN A 133 1 17 HELIX 5 5 THR A 139 LYS A 141 5 3 HELIX 6 6 HIS A 146 ALA A 150 1 5 HELIX 7 7 PRO A 162 GLY A 170 1 9 HELIX 8 8 ASP A 176 ASP A 190 1 15 HELIX 9 9 PRO A 194 GLY A 206 1 13 HELIX 10 10 ASP A 214 ARG A 230 1 17 HELIX 11 11 ASP A 239 TYR A 253 1 15 HELIX 12 12 ASP B 30 THR B 40 1 11 HELIX 13 13 ASP B 54 ALA B 60 1 7 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 5 PHE A 68 ASN A 69 0 SHEET 2 AA 5 TYR A 47 ILE A 49 -1 O LEU A 48 N PHE A 68 SHEET 3 AA 5 SER A 95 ILE A 100 1 O GLY A 97 N TYR A 47 SHEET 4 AA 5 PHE A 21 TYR A 26 1 O PHE A 21 N ILE A 96 SHEET 5 AA 5 VAL A 143 GLY A 145 1 O VAL A 144 N LEU A 24 SHEET 1 AB 2 ASP A 75 ALA A 77 0 SHEET 2 AB 2 TYR B 15 LYS B 17 -1 O GLY B 16 N ARG A 76 SHEET 1 AC 2 ARG A 105 ASP A 106 0 SHEET 2 AC 2 PHE A 111 THR A 112 -1 O THR A 112 N ARG A 105 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 SHEET 1 BB 2 ARG B 105 ASP B 107 0 SHEET 2 BB 2 VAL B 110 THR B 112 -1 O VAL B 110 N ASP B 107 LINK C ALA C 1 N FGA C 2 1555 1555 1.43 LINK CD FGA C 2 N 6CL C 3 1555 1555 1.44 LINK C 6CL C 3 N DAL C 4 1555 1555 1.42 LINK C ALA D 1 N FGA D 2 1555 1555 1.41 LINK CD FGA D 2 N 6CL D 3 1555 1555 1.40 LINK C 6CL D 3 N DAL D 4 1555 1555 1.42 LINK O4 MAG E 1 C1 NAG E 2 1555 1555 1.42 LINK O4 NAG E 2 C1 NAG E 3 1555 1555 1.45 LINK O4 MAG F 1 C1 NAG F 2 1555 1555 1.40 LINK O4 NAG F 2 C1 NAG F 3 1555 1555 1.42 LINK ND1 HIS A 25 ZN ZN A1260 1555 1555 2.46 LINK ND1 HIS A 146 ZN ZN A1260 1555 1555 2.45 LINK OD2 ASP A 156 ZN ZN A1260 1555 1555 2.40 LINK ZN ZN A1260 O HOH A2005 1555 1555 2.44 LINK ND1 HIS B 25 ZN ZN B1256 1555 1555 2.04 LINK ND1 HIS B 146 ZN ZN B1256 1555 1555 2.43 LINK OD2 ASP B 156 ZN ZN B1256 1555 1555 2.41 LINK ZN ZN B1256 O HOH B2008 1555 1555 2.43 CISPEP 1 ASP A 108 GLY A 109 0 3.05 CISPEP 2 ASP A 156 PRO A 157 0 2.06 CISPEP 3 GLY B 64 GLN B 65 0 -5.21 CISPEP 4 ASP B 108 GLY B 109 0 -2.43 CISPEP 5 VAL B 151 GLY B 152 0 -18.44 CISPEP 6 ASP B 156 PRO B 157 0 4.90 CISPEP 7 6CL C 3 DAL C 4 0 -0.34 CISPEP 8 6CL D 3 DAL D 4 0 1.93 CRYST1 101.186 101.186 162.261 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 0.009883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009883 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006163 0.00000