HEADER HYDROLASE 17-JUN-10 3NJN TITLE Q118A MUTANT OF SO1698 PROTEIN, AN ASPARTIC PEPTIDASE FROM SHEWANELLA TITLE 2 ONEIDENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN 1-116; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PEPTIDASE; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: C-TERMINAL DOMAIN 117-125; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS; SOURCE 3 ORGANISM_TAXID: 70863; SOURCE 4 STRAIN: MR-1; SOURCE 5 GENE: SO_1698; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS; SOURCE 13 ORGANISM_TAXID: 70863; SOURCE 14 STRAIN: MR-1; SOURCE 15 GENE: SO_1698; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS STRUCTURAL GENOMICS, ASPARTIC PEPTIDASE, AUTOCATALYSIS, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, MCSG, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.OSIPIUK,R.MULLIGAN,M.BARGASSA,F.COLLART,A.JOACHIMIAK,MIDWEST CENTER AUTHOR 2 FOR STRUCTURAL GENOMICS (MCSG) REVDAT 5 06-SEP-23 3NJN 1 REMARK SEQADV LINK REVDAT 4 08-NOV-17 3NJN 1 REMARK REVDAT 3 31-OCT-12 3NJN 1 LINK REVDAT 2 10-OCT-12 3NJN 1 JRNL VERSN REVDAT 1 21-JUL-10 3NJN 0 JRNL AUTH J.OSIPIUK,R.MULLIGAN,M.BARGASSA,J.E.HAMILTON,M.A.CUNNINGHAM, JRNL AUTH 2 A.JOACHIMIAK JRNL TITL CHARACTERIZATION OF MEMBER OF DUF1888 PROTEIN FAMILY, JRNL TITL 2 SELF-CLEAVING AND SELF-ASSEMBLING ENDOPEPTIDASE. JRNL REF J.BIOL.CHEM. V. 287 19452 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22493430 JRNL DOI 10.1074/JBC.M112.358069 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 64392 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2580 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2745 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.3420 REMARK 3 BIN FREE R VALUE SET COUNT : 112 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1821 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 293 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : -0.54000 REMARK 3 B12 (A**2) : 0.18000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.043 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.025 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2008 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1300 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2772 ; 1.713 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3262 ; 0.955 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 6.266 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;44.851 ;26.627 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 344 ;13.591 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;28.896 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 350 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2239 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 361 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1269 ; 1.855 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 518 ; 0.587 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2102 ; 2.839 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 739 ; 3.728 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 648 ; 5.495 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3308 ; 1.524 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 116 REMARK 3 ORIGIN FOR THE GROUP (A): -4.4411 20.8966 102.6252 REMARK 3 T TENSOR REMARK 3 T11: 0.0705 T22: 0.0572 REMARK 3 T33: 0.0639 T12: -0.0030 REMARK 3 T13: 0.0020 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.3449 L22: 0.0678 REMARK 3 L33: 0.2515 L12: -0.1318 REMARK 3 L13: 0.0011 L23: 0.0245 REMARK 3 S TENSOR REMARK 3 S11: -0.0031 S12: 0.0242 S13: -0.0488 REMARK 3 S21: 0.0025 S22: -0.0037 S23: 0.0149 REMARK 3 S31: 0.0341 S32: -0.0017 S33: 0.0068 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 117 B 124 REMARK 3 ORIGIN FOR THE GROUP (A): -3.1626 9.2042 111.9560 REMARK 3 T TENSOR REMARK 3 T11: 0.1059 T22: 0.0269 REMARK 3 T33: 0.1680 T12: 0.0055 REMARK 3 T13: 0.0751 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 3.3722 L22: 2.0545 REMARK 3 L33: 1.9153 L12: -2.5086 REMARK 3 L13: 2.4973 L23: -1.6753 REMARK 3 S TENSOR REMARK 3 S11: 0.0787 S12: 0.0180 S13: -0.2458 REMARK 3 S21: -0.0797 S22: -0.0427 S23: 0.1908 REMARK 3 S31: 0.1214 S32: -0.0347 S33: -0.0360 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 3 C 116 REMARK 3 ORIGIN FOR THE GROUP (A): -20.2246 34.1382 111.4885 REMARK 3 T TENSOR REMARK 3 T11: 0.0541 T22: 0.0705 REMARK 3 T33: 0.0603 T12: -0.0032 REMARK 3 T13: 0.0016 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.0852 L22: 0.2524 REMARK 3 L33: 0.4344 L12: -0.0848 REMARK 3 L13: -0.0445 L23: -0.0448 REMARK 3 S TENSOR REMARK 3 S11: 0.0017 S12: 0.0097 S13: -0.0102 REMARK 3 S21: 0.0073 S22: 0.0002 S23: 0.0344 REMARK 3 S31: -0.0007 S32: -0.0652 S33: -0.0019 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 117 D 124 REMARK 3 ORIGIN FOR THE GROUP (A): -30.8265 32.3701 102.8467 REMARK 3 T TENSOR REMARK 3 T11: 0.0445 T22: 0.1183 REMARK 3 T33: 0.0606 T12: 0.0022 REMARK 3 T13: -0.0042 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 4.1388 L22: 3.7190 REMARK 3 L33: 5.7276 L12: -3.0779 REMARK 3 L13: 4.8014 L23: -2.9320 REMARK 3 S TENSOR REMARK 3 S11: 0.0337 S12: -0.2969 S13: -0.0673 REMARK 3 S21: -0.0603 S22: -0.0255 S23: 0.2198 REMARK 3 S31: 0.0930 S32: -0.4248 S33: -0.0082 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3NJN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000059912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64712 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 23.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.50700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.190 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3N55 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CALCIUM CHLORIDE, 0.1 M BIS-TRIS REMARK 280 BUFFER, 45% 2-METHYL-2,4-PENTANEDIOL, PH 5.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 36.17550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 20.88593 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 85.33600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 36.17550 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 20.88593 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 85.33600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 36.17550 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 20.88593 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 85.33600 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 36.17550 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 20.88593 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 85.33600 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 36.17550 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 20.88593 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 85.33600 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 36.17550 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 20.88593 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 85.33600 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 41.77187 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 170.67200 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 41.77187 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 170.67200 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 41.77187 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 170.67200 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 41.77187 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 170.67200 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 41.77187 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 170.67200 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 41.77187 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 170.67200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -178.0 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 -0.500000 -0.866025 0.000000 36.17550 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 62.65780 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -36.17550 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 62.65780 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 5390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 REMARK 350 BIOMOLECULE: 3 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: 4780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 -36.17550 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 62.65780 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CA CA A 403 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 133 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 269 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 119 LIES ON A SPECIAL POSITION. 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 PHE A 2 REMARK 465 ASN B 125 REMARK 465 SER C -2 REMARK 465 ASN C -1 REMARK 465 ALA C 0 REMARK 465 MET C 1 REMARK 465 PHE C 2 REMARK 465 GLN D 124 REMARK 465 ASN D 125 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 184 O HOH A 274 2.13 REMARK 500 O THR A 54 O HOH A 161 2.15 REMARK 500 O HOH C 223 O HOH C 247 2.16 REMARK 500 O HOH A 197 O HOH A 285 2.17 REMARK 500 O HOH A 204 O HOH A 250 2.19 REMARK 500 O HOH C 213 O HOH C 237 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 238 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 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 17 O REMARK 620 2 GLU A 18 OE1 100.5 REMARK 620 3 HOH A 146 O 88.3 75.2 REMARK 620 4 HOH A 269 O 83.0 142.3 67.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 52 O REMARK 620 2 HOH C 142 O 158.1 REMARK 620 3 HOH C 152 O 79.4 94.0 REMARK 620 4 HOH C 166 O 131.3 65.7 139.7 REMARK 620 5 HOH C 177 O 89.2 86.7 151.0 66.0 REMARK 620 6 HOH C 180 O 74.4 126.6 116.1 63.0 85.6 REMARK 620 7 HOH C 210 O 81.5 76.6 74.2 128.0 77.9 150.9 REMARK 620 8 HOH C 276 O 120.1 76.3 71.7 69.9 135.9 73.5 134.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3N55 RELATED DB: PDB REMARK 900 WILD-TYPE SO1698 PROTEIN, AN ASPARTIC PEPTIDASE FROM SHEWANELLA REMARK 900 ONEIDENSIS. REMARK 900 RELATED ID: 3NJF RELATED DB: PDB REMARK 900 RELATED ID: 3NJG RELATED DB: PDB REMARK 900 RELATED ID: 3NJH RELATED DB: PDB REMARK 900 RELATED ID: 3NJI RELATED DB: PDB REMARK 900 RELATED ID: 3NJJ RELATED DB: PDB REMARK 900 RELATED ID: 3NJK RELATED DB: PDB REMARK 900 RELATED ID: 3NJL RELATED DB: PDB REMARK 900 RELATED ID: 3NJM RELATED DB: PDB REMARK 900 RELATED ID: APC83618 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CHAIN-B PEPTIDE IS A PRODUCT OF AUTOCATALYTIC CLEAVAGE DURING REMARK 999 CRYSTALLIZATION DBREF 3NJN A 1 116 UNP Q8EGA7 Q8EGA7_SHEON 1 116 DBREF 3NJN B 117 125 UNP Q8EGA7 Q8EGA7_SHEON 117 125 DBREF 3NJN C 1 116 UNP Q8EGA7 Q8EGA7_SHEON 1 116 DBREF 3NJN D 117 125 UNP Q8EGA7 Q8EGA7_SHEON 117 125 SEQADV 3NJN SER A -2 UNP Q8EGA7 EXPRESSION TAG SEQADV 3NJN ASN A -1 UNP Q8EGA7 EXPRESSION TAG SEQADV 3NJN ALA A 0 UNP Q8EGA7 EXPRESSION TAG SEQADV 3NJN ALA B 118 UNP Q8EGA7 GLN 118 ENGINEERED MUTATION SEQADV 3NJN SER C -2 UNP Q8EGA7 EXPRESSION TAG SEQADV 3NJN ASN C -1 UNP Q8EGA7 EXPRESSION TAG SEQADV 3NJN ALA C 0 UNP Q8EGA7 EXPRESSION TAG SEQADV 3NJN ALA D 118 UNP Q8EGA7 GLN 118 ENGINEERED MUTATION SEQRES 1 A 119 SER ASN ALA MET PHE ALA PRO GLN GLY LEU ALA GLN PHE SEQRES 2 A 119 ILE LYS VAL ASN VAL THR LEU GLU ASN GLY GLU PRO VAL SEQRES 3 A 119 PHE ILE TYR THR ASP ALA ASN GLY GLN VAL CYS GLN GLY SEQRES 4 A 119 ASP ILE THR VAL THR GLN ALA GLY THR ILE THR TYR LEU SEQRES 5 A 119 LEU ASN ASP GLN THR LEU LYS GLY LEU LYS PHE VAL GLY SEQRES 6 A 119 VAL GLY PHE VAL THR PRO PHE ASP GLY ILE ILE ASP ALA SEQRES 7 A 119 VAL THR ILE SER SER ASP GLY MET LEU VAL GLN LEU VAL SEQRES 8 A 119 ASP LEU ASP LYS THR PRO GLY THR THR LYS PHE GLN PHE SEQRES 9 A 119 VAL LEU SER ASN THR ALA ASN THR LEU LEU VAL LEU SER SEQRES 10 A 119 PRO ASP SEQRES 1 B 9 PRO ALA ILE ILE ASN ARG PRO GLN ASN SEQRES 1 C 119 SER ASN ALA MET PHE ALA PRO GLN GLY LEU ALA GLN PHE SEQRES 2 C 119 ILE LYS VAL ASN VAL THR LEU GLU ASN GLY GLU PRO VAL SEQRES 3 C 119 PHE ILE TYR THR ASP ALA ASN GLY GLN VAL CYS GLN GLY SEQRES 4 C 119 ASP ILE THR VAL THR GLN ALA GLY THR ILE THR TYR LEU SEQRES 5 C 119 LEU ASN ASP GLN THR LEU LYS GLY LEU LYS PHE VAL GLY SEQRES 6 C 119 VAL GLY PHE VAL THR PRO PHE ASP GLY ILE ILE ASP ALA SEQRES 7 C 119 VAL THR ILE SER SER ASP GLY MET LEU VAL GLN LEU VAL SEQRES 8 C 119 ASP LEU ASP LYS THR PRO GLY THR THR LYS PHE GLN PHE SEQRES 9 C 119 VAL LEU SER ASN THR ALA ASN THR LEU LEU VAL LEU SER SEQRES 10 C 119 PRO ASP SEQRES 1 D 9 PRO ALA ILE ILE ASN ARG PRO GLN ASN HET MPD A 401 8 HET CA A 403 1 HET CA C 402 1 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM CA CALCIUM ION FORMUL 5 MPD C6 H14 O2 FORMUL 6 CA 2(CA 2+) FORMUL 8 HOH *293(H2 O) SHEET 1 A 6 VAL A 33 CYS A 34 0 SHEET 2 A 6 GLU A 21 THR A 27 -1 N TYR A 26 O CYS A 34 SHEET 3 A 6 LEU A 7 GLU A 18 -1 N LYS A 12 O THR A 27 SHEET 4 A 6 GLY A 44 ASP A 52 1 O LEU A 49 N VAL A 13 SHEET 5 A 6 LEU A 84 ASP A 89 -1 O VAL A 85 N TYR A 48 SHEET 6 A 6 ALA A 75 ILE A 78 -1 N THR A 77 O GLN A 86 SHEET 1 B 9 ILE A 38 VAL A 40 0 SHEET 2 B 9 ALA B 118 ASN B 121 1 O ILE B 120 N VAL A 40 SHEET 3 B 9 GLY A 95 SER A 104 -1 N GLY A 95 O ASN B 121 SHEET 4 B 9 LEU A 111 LEU A 113 -1 O VAL A 112 N LEU A 103 SHEET 5 B 9 LYS C 59 PHE C 65 1 O VAL C 63 N LEU A 111 SHEET 6 B 9 GLN C 100 SER C 104 -1 O GLN C 100 N GLY C 64 SHEET 7 B 9 LEU C 111 LEU C 113 -1 O VAL C 112 N LEU C 103 SHEET 8 B 9 LYS A 59 PHE A 65 1 N VAL A 63 O LEU C 111 SHEET 9 B 9 GLY A 95 SER A 104 -1 O VAL A 102 N VAL A 61 SHEET 1 C 6 VAL C 33 CYS C 34 0 SHEET 2 C 6 GLU C 21 THR C 27 -1 N TYR C 26 O CYS C 34 SHEET 3 C 6 LEU C 7 GLU C 18 -1 N LYS C 12 O THR C 27 SHEET 4 C 6 GLY C 44 ASP C 52 1 O LEU C 49 N VAL C 13 SHEET 5 C 6 LEU C 84 ASP C 89 -1 O VAL C 85 N TYR C 48 SHEET 6 C 6 ALA C 75 ILE C 78 -1 N THR C 77 O GLN C 86 SHEET 1 D 3 ILE C 38 VAL C 40 0 SHEET 2 D 3 ALA D 118 ASN D 121 1 O ILE D 120 N VAL C 40 SHEET 3 D 3 GLY C 95 LYS C 98 -1 N GLY C 95 O ASN D 121 LINK NZ LYS A 98 C ASP A 116 1555 1555 1.32 LINK NZ LYS C 98 C ASP C 116 1555 1555 1.32 LINK O LEU A 17 CA CA A 403 1555 1555 2.24 LINK OE1 GLU A 18 CA CA A 403 1555 1555 2.27 LINK O HOH A 146 CA CA A 403 1555 1555 2.44 LINK O HOH A 269 CA CA A 403 1555 1555 2.19 LINK O ASP C 52 CA CA C 402 1555 1555 2.36 LINK O HOH C 142 CA CA C 402 1555 1555 2.36 LINK O HOH C 152 CA CA C 402 1555 1555 2.44 LINK O HOH C 166 CA CA C 402 1555 1555 2.70 LINK O HOH C 177 CA CA C 402 1555 1555 2.37 LINK O HOH C 180 CA CA C 402 1555 1555 2.35 LINK O HOH C 210 CA CA C 402 1555 1555 2.49 LINK O HOH C 276 CA CA C 402 1555 1555 2.46 SITE 1 AC1 4 ASN A 14 GLN A 53 HOH A 119 HOH A 133 SITE 1 AC2 4 LEU A 17 GLU A 18 HOH A 146 HOH A 269 SITE 1 AC3 8 ASP C 52 HOH C 142 HOH C 152 HOH C 166 SITE 2 AC3 8 HOH C 177 HOH C 180 HOH C 210 HOH C 276 CRYST1 72.351 72.351 256.008 90.00 90.00 120.00 H 3 2 36 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 0.013822 0.007980 0.000000 0.00000 SCALE2 0.000000 0.015960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003906 0.00000