HEADER HYDROLASE 15-APR-16 5JD8 TITLE CRYSTAL STRUCTURE OF THE SERINE ENDOPROTEASE FROM YERSINIA PESTIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC SERINE PEPTIDASE DEGS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 29-362; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS CO92; SOURCE 3 ORGANISM_TAXID: 214092; SOURCE 4 GENE: DEGS, AK38_3169; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-MAGIC; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG53 KEYWDS DEGS, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF KEYWDS 2 INFECTIOUS DISEASES, CSGID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.V.FILIPPOVA,Z.WAWRZSAK,J.SANDOVAL,T.SKARINA,S.GRIMSHAW,A.SAVCHENKO, AUTHOR 2 W.F.ANDERSON,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 3 (CSGID) REVDAT 3 27-SEP-23 5JD8 1 REMARK REVDAT 2 22-NOV-17 5JD8 1 REMARK REVDAT 1 04-MAY-16 5JD8 0 JRNL AUTH E.V.FILIPPOVA,Z.WAWRZSAK,J.SANDOVAL,T.SKARINA,S.GRIMSHAW, JRNL AUTH 2 A.SAVCHENKO,W.F.ANDERSON, JRNL AUTH 3 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES JRNL AUTH 4 (CSGID) JRNL TITL CRYSTAL STRUCTURE OF THE SERINE ENDOPROTEASE FROM YERSINIA JRNL TITL 2 PESTIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25187 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1292 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1871 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2017 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 1.24000 REMARK 3 B12 (A**2) : -0.19000 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): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.311 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2081 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2115 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2828 ; 2.003 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4843 ; 1.048 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 271 ; 7.236 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;37.475 ;25.375 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 354 ;15.738 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;14.846 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 355 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2347 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 424 ; 0.002 ; 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): 1093 ; 2.333 ; 3.234 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1092 ; 2.331 ; 3.233 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1361 ; 3.809 ; 4.815 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1362 ; 3.808 ; 4.817 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 988 ; 2.889 ; 3.643 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 984 ; 2.881 ; 3.627 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1462 ; 4.613 ; 5.293 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2188 ; 7.968 ;25.624 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2189 ; 7.966 ;25.631 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL 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 : 7 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 43 A 134 REMARK 3 ORIGIN FOR THE GROUP (A): 20.7007 47.0656 50.4939 REMARK 3 T TENSOR REMARK 3 T11: 0.0449 T22: 0.0582 REMARK 3 T33: 0.1295 T12: 0.0177 REMARK 3 T13: 0.0352 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 0.6618 L22: 1.6535 REMARK 3 L33: 0.6275 L12: -0.9985 REMARK 3 L13: -0.4222 L23: 0.5667 REMARK 3 S TENSOR REMARK 3 S11: 0.0269 S12: 0.0132 S13: 0.0847 REMARK 3 S21: -0.0401 S22: -0.0615 S23: -0.2294 REMARK 3 S31: 0.0304 S32: -0.0033 S33: 0.0346 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 : A 135 A 234 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2108 49.3535 53.9369 REMARK 3 T TENSOR REMARK 3 T11: 0.0695 T22: 0.0581 REMARK 3 T33: 0.0901 T12: 0.0086 REMARK 3 T13: 0.0109 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.9328 L22: 0.3945 REMARK 3 L33: 0.0866 L12: -0.3613 REMARK 3 L13: -0.0821 L23: 0.0366 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: 0.0397 S13: -0.1135 REMARK 3 S21: -0.0398 S22: -0.0190 S23: -0.0138 REMARK 3 S31: -0.0046 S32: -0.0039 S33: 0.0061 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 : A 235 A 263 REMARK 3 ORIGIN FOR THE GROUP (A): 10.9532 29.2172 49.0316 REMARK 3 T TENSOR REMARK 3 T11: 0.1153 T22: 0.0315 REMARK 3 T33: 0.2080 T12: -0.0068 REMARK 3 T13: 0.0728 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 1.7129 L22: 0.7304 REMARK 3 L33: 1.5592 L12: 0.6593 REMARK 3 L13: -1.1471 L23: 0.1706 REMARK 3 S TENSOR REMARK 3 S11: -0.2290 S12: 0.1031 S13: -0.2919 REMARK 3 S21: 0.0298 S22: -0.0235 S23: -0.0731 REMARK 3 S31: 0.3011 S32: -0.1717 S33: 0.2526 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 : A 280 A 311 REMARK 3 ORIGIN FOR THE GROUP (A): -3.2743 15.7487 39.0372 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.2412 REMARK 3 T33: 0.1847 T12: -0.1696 REMARK 3 T13: 0.0525 T23: -0.1444 REMARK 3 L TENSOR REMARK 3 L11: 1.8574 L22: 6.5303 REMARK 3 L33: 4.6532 L12: -1.0756 REMARK 3 L13: 2.3675 L23: 1.6216 REMARK 3 S TENSOR REMARK 3 S11: 0.2295 S12: -0.0797 S13: -0.3372 REMARK 3 S21: -0.2508 S22: -0.1217 S23: 0.6236 REMARK 3 S31: 0.3500 S32: -0.3537 S33: -0.1078 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 312 A 329 REMARK 3 ORIGIN FOR THE GROUP (A): 2.2785 21.2240 47.5389 REMARK 3 T TENSOR REMARK 3 T11: 0.1491 T22: 0.1241 REMARK 3 T33: 0.0759 T12: -0.1294 REMARK 3 T13: 0.0863 T23: -0.0714 REMARK 3 L TENSOR REMARK 3 L11: 10.2623 L22: 5.6193 REMARK 3 L33: 1.3582 L12: -5.7164 REMARK 3 L13: 0.2231 L23: 1.6170 REMARK 3 S TENSOR REMARK 3 S11: 0.0425 S12: -0.2805 S13: -0.1101 REMARK 3 S21: 0.1902 S22: -0.1219 S23: 0.0546 REMARK 3 S31: 0.2700 S32: -0.3007 S33: 0.0794 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 330 A 343 REMARK 3 ORIGIN FOR THE GROUP (A): -6.7713 8.2840 42.0678 REMARK 3 T TENSOR REMARK 3 T11: 0.1592 T22: 0.3536 REMARK 3 T33: 0.2497 T12: -0.2096 REMARK 3 T13: 0.0099 T23: -0.1333 REMARK 3 L TENSOR REMARK 3 L11: 1.0000 L22: 5.2483 REMARK 3 L33: 0.0630 L12: 2.2744 REMARK 3 L13: 0.1095 L23: 0.2973 REMARK 3 S TENSOR REMARK 3 S11: 0.0736 S12: -0.0238 S13: -0.3447 REMARK 3 S21: 0.1557 S22: -0.1140 S23: -0.6902 REMARK 3 S31: 0.0572 S32: -0.1196 S33: 0.0404 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 344 A 351 REMARK 3 ORIGIN FOR THE GROUP (A): 8.2619 16.1766 42.7082 REMARK 3 T TENSOR REMARK 3 T11: 0.1869 T22: 0.2864 REMARK 3 T33: 0.1614 T12: 0.0306 REMARK 3 T13: -0.0006 T23: -0.1881 REMARK 3 L TENSOR REMARK 3 L11: 4.4755 L22: 6.8992 REMARK 3 L33: 0.3442 L12: 3.1264 REMARK 3 L13: 0.3714 L23: 1.0635 REMARK 3 S TENSOR REMARK 3 S11: 0.0862 S12: 0.7828 S13: -0.3954 REMARK 3 S21: 0.4781 S22: 0.0299 S23: -0.0422 REMARK 3 S31: 0.1737 S32: 0.1044 S33: -0.1161 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 REMARK 4 REMARK 4 5JD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : BERYLLIUM LENSES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26479 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.65000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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: 4RQY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 10% ISOPROPANE, 50 MM REMARK 280 CAPSO BUFFER PH 11, 0.1 M SODIUM CITRATE PH 5.6, 5% P200 REMARK 280 PARATONE-N OIL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+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 1.000000 0.000000 0.000000 52.20900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.14288 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.33833 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 52.20900 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 30.14288 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.33833 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 52.20900 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 30.14288 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.33833 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 60.28576 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 50.67667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 60.28576 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 50.67667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 60.28576 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 50.67667 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 52.20900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 90.42864 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -52.20900 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 90.42864 REMARK 350 BIOMT3 3 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 S SO4 A 403 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 553 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 PRO A 29 REMARK 465 GLY A 30 REMARK 465 TYR A 31 REMARK 465 LEU A 32 REMARK 465 PHE A 33 REMARK 465 SER A 34 REMARK 465 GLY A 35 REMARK 465 LYS A 36 REMARK 465 SER A 37 REMARK 465 ASN A 38 REMARK 465 ASN A 39 REMARK 465 VAL A 40 REMARK 465 ASN A 41 REMARK 465 GLU A 42 REMARK 465 SER A 68 REMARK 465 ALA A 69 REMARK 465 THR A 70 REMARK 465 GLN A 71 REMARK 465 GLN A 72 REMARK 465 GLY A 73 REMARK 465 LEU A 74 REMARK 465 GLY A 179 REMARK 465 LEU A 180 REMARK 465 SER A 181 REMARK 465 SER A 182 REMARK 465 SER A 183 REMARK 465 GLY A 184 REMARK 465 ARG A 185 REMARK 465 GLN A 186 REMARK 465 ASP A 220 REMARK 465 LYS A 221 REMARK 465 SER A 222 REMARK 465 ASN A 223 REMARK 465 ASN A 224 REMARK 465 GLY A 225 REMARK 465 GLU A 264 REMARK 465 TYR A 265 REMARK 465 PRO A 266 REMARK 465 PRO A 267 REMARK 465 PHE A 268 REMARK 465 ASN A 269 REMARK 465 ALA A 270 REMARK 465 ASN A 271 REMARK 465 ASP A 272 REMARK 465 ASN A 273 REMARK 465 GLY A 274 REMARK 465 SER A 275 REMARK 465 ASP A 276 REMARK 465 ARG A 277 REMARK 465 VAL A 278 REMARK 465 HIS A 279 REMARK 465 GLN A 352 REMARK 465 ASN A 353 REMARK 465 GLU A 354 REMARK 465 MET A 355 REMARK 465 LEU A 356 REMARK 465 THR A 357 REMARK 465 THR A 358 REMARK 465 GLN A 359 REMARK 465 ALA A 360 REMARK 465 ALA A 361 REMARK 465 ASP A 362 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 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = -3.4 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 ALA A 134 46.92 -94.73 REMARK 500 THR A 216 -50.28 -124.70 REMARK 500 GLN A 294 21.55 -77.02 REMARK 500 ASN A 307 61.61 33.34 REMARK 500 ASN A 337 75.70 50.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CXS A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP02413 RELATED DB: TARGETTRACK DBREF1 5JD8 A 29 362 UNP A0A0B6NK33_YERPE DBREF2 5JD8 A A0A0B6NK33 29 362 SEQRES 1 A 334 PRO GLY TYR LEU PHE SER GLY LYS SER ASN ASN VAL ASN SEQRES 2 A 334 GLU GLU VAL PRO THR SER TYR ASN GLN ALA VAL ARG ARG SEQRES 3 A 334 ALA ALA PRO ALA VAL VAL ASN VAL TYR ASN ARG SER LEU SEQRES 4 A 334 SER ALA THR GLN GLN GLY LEU ALA ILE ARG THR LEU GLY SEQRES 5 A 334 SER GLY VAL ILE MET SER ASP LYS GLY TYR ILE LEU THR SEQRES 6 A 334 ASN LYS HIS VAL ILE ASN ASP ALA GLU GLN ILE ILE VAL SEQRES 7 A 334 ALA MET GLN ASN GLY ARG ILE SER GLU ALA LEU LEU VAL SEQRES 8 A 334 GLY SER ASP ASN LEU THR ASP LEU ALA VAL LEU LYS ILE SEQRES 9 A 334 ASP ALA THR ASN LEU PRO VAL ILE PRO ILE ASN ILE ASN SEQRES 10 A 334 ARG THR PRO HIS ILE GLY ASP VAL VAL LEU ALA ILE GLY SEQRES 11 A 334 ASN PRO TYR ASN LEU GLY GLN THR VAL THR GLN GLY ILE SEQRES 12 A 334 ILE SER ALA THR GLY ARG ILE GLY LEU SER SER SER GLY SEQRES 13 A 334 ARG GLN ASN PHE LEU GLN THR ASP ALA SER ILE ASN GLN SEQRES 14 A 334 GLY ASN SER GLY GLY ALA LEU VAL ASN THR LEU GLY GLU SEQRES 15 A 334 LEU MET GLY ILE ASN THR LEU SER PHE ASP LYS SER ASN SEQRES 16 A 334 ASN GLY GLU THR PRO GLU GLY ILE GLY PHE ALA ILE PRO SEQRES 17 A 334 THR ALA LEU ALA THR LYS VAL MET GLU LYS LEU ILE ARG SEQRES 18 A 334 ASP GLY ARG VAL ILE ARG GLY TYR ILE GLY ILE THR GLY SEQRES 19 A 334 GLU GLU TYR PRO PRO PHE ASN ALA ASN ASP ASN GLY SER SEQRES 20 A 334 ASP ARG VAL HIS GLY ILE LYS VAL LYS LYS VAL SER PRO SEQRES 21 A 334 ASP GLY PRO ALA ALA GLN ALA GLY ILE HIS VAL GLY ASP SEQRES 22 A 334 ILE ILE LEU ASN VAL ASN ASN LYS PRO ALA THR SER VAL SEQRES 23 A 334 ILE GLU THR MET ASP GLN VAL ALA GLU VAL ARG PRO GLY SEQRES 24 A 334 THR THR ILE PRO VAL LEU LEU LEU ARG ASN GLY GLN GLN SEQRES 25 A 334 ILE ALA VAL GLN ILE THR ILE THR GLU LEU ASP GLN ASN SEQRES 26 A 334 GLU MET LEU THR THR GLN ALA ALA ASP HET CXS A 401 14 HET PEG A 402 7 HET SO4 A 403 5 HETNAM CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM SO4 SULFATE ION FORMUL 2 CXS C9 H19 N O3 S FORMUL 3 PEG C4 H10 O3 FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *154(H2 O) HELIX 1 AA1 TYR A 48 ALA A 56 1 9 HELIX 2 AA2 LYS A 95 ASN A 99 1 5 HELIX 3 AA3 ASN A 159 LEU A 163 5 5 HELIX 4 AA4 THR A 237 GLY A 251 1 15 HELIX 5 AA5 ALA A 292 GLY A 296 5 5 HELIX 6 AA6 SER A 313 VAL A 324 1 12 SHEET 1 AA1 7 VAL A 59 ARG A 65 0 SHEET 2 AA1 7 ILE A 76 ILE A 84 -1 O GLY A 80 N VAL A 62 SHEET 3 AA1 7 TYR A 90 ASN A 94 -1 O LEU A 92 N VAL A 83 SHEET 4 AA1 7 LEU A 127 LYS A 131 -1 O LEU A 130 N ILE A 91 SHEET 5 AA1 7 ILE A 113 ASP A 122 -1 N VAL A 119 O VAL A 129 SHEET 6 AA1 7 GLN A 103 ALA A 107 -1 N VAL A 106 O SER A 114 SHEET 7 AA1 7 VAL A 59 ARG A 65 -1 N ASN A 61 O ALA A 107 SHEET 1 AA2 7 VAL A 153 GLY A 158 0 SHEET 2 AA2 7 THR A 166 THR A 175 -1 O THR A 166 N GLY A 158 SHEET 3 AA2 7 LEU A 189 THR A 191 -1 O GLN A 190 N SER A 173 SHEET 4 AA2 7 GLY A 232 PRO A 236 -1 O ALA A 234 N LEU A 189 SHEET 5 AA2 7 LEU A 211 SER A 218 -1 N THR A 216 O PHE A 233 SHEET 6 AA2 7 ALA A 203 ASN A 206 -1 N LEU A 204 O MET A 212 SHEET 7 AA2 7 VAL A 153 GLY A 158 -1 N ILE A 157 O ALA A 203 SHEET 1 AA3 6 GLY A 256 TYR A 257 0 SHEET 2 AA3 6 GLN A 340 GLU A 349 -1 O THR A 348 N TYR A 257 SHEET 3 AA3 6 THR A 328 LEU A 335 -1 N THR A 328 O ILE A 347 SHEET 4 AA3 6 ILE A 302 VAL A 306 -1 N LEU A 304 O LEU A 333 SHEET 5 AA3 6 ILE A 281 VAL A 286 -1 N ILE A 281 O ILE A 303 SHEET 6 AA3 6 ILE A 260 GLU A 263 -1 N THR A 261 O LYS A 285 SHEET 1 AA4 5 GLY A 256 TYR A 257 0 SHEET 2 AA4 5 GLN A 340 GLU A 349 -1 O THR A 348 N TYR A 257 SHEET 3 AA4 5 THR A 328 LEU A 335 -1 N THR A 328 O ILE A 347 SHEET 4 AA4 5 ILE A 302 VAL A 306 -1 N LEU A 304 O LEU A 333 SHEET 5 AA4 5 LYS A 309 PRO A 310 -1 O LYS A 309 N VAL A 306 SITE 1 AC1 7 GLU A 102 GLU A 115 ALA A 116 ASN A 145 SITE 2 AC1 7 ARG A 146 THR A 147 HIS A 149 SITE 1 AC2 5 VAL A 44 PRO A 45 THR A 46 SER A 47 SITE 2 AC2 5 HOH A 510 SITE 1 AC3 3 TYR A 48 VAL A 153 GLN A 169 CRYST1 104.418 104.418 76.015 90.00 90.00 120.00 H 3 9 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 0.009577 0.005529 0.000000 0.00000 SCALE2 0.000000 0.011058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013155 0.00000