HEADER HYDROLASE 16-JUN-08 3DH2 TITLE CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH GUANOSINE-3'-CYCLOPHOSPHATE TITLE 2 PREPARED BY COCRYSTALLIZATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: RIBONUCLEASE SA2; COMPND 5 EC: 3.1.4.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AUREOFACIENS; SOURCE 3 ORGANISM_TAXID: 1894; SOURCE 4 STRAIN: R8/26; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NOVA BLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PEH200 KEYWDS RIBONUCLEASE, HYDROLASE, PROTEIN-MONONUCLEOTIDE COMPLEX, GUANOSINE- KEYWDS 2 3'-MONOPHOSPHATE, MONONUCLEOTIDE, COCRYSTALLIZATION EXPDTA X-RAY DIFFRACTION AUTHOR J.SEVCIK,V.BAUEROVA-HLINKOVA REVDAT 4 29-JUL-20 3DH2 1 COMPND REMARK HETNAM SITE REVDAT 3 13-JUL-11 3DH2 1 VERSN REVDAT 2 04-AUG-09 3DH2 1 JRNL REVDAT 1 16-JUN-09 3DH2 0 JRNL AUTH V.BAUEROVA-HLINKOVA,R.DVORSKY,D.PERECKO,F.POVAZANEC,J.SEVCIK JRNL TITL STRUCTURE OF RNASE SA2 COMPLEXES WITH MONONUCLEOTIDES - NEW JRNL TITL 2 ASPECTS OF CATALYTIC REACTION AND SUBSTRATE RECOGNITION JRNL REF FEBS J. V. 276 4156 2009 JRNL REFN ISSN 1742-464X JRNL PMID 19558492 JRNL DOI 10.1111/J.1742-4658.2009.07125.X REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 15526 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 821 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 937 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3030 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 137 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.94000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -0.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.45000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.556 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.277 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.214 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.915 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3284 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4491 ; 1.604 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 7.496 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;33.940 ;23.140 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 473 ;19.149 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;21.946 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 460 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2601 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1512 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2174 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 214 ; 0.192 ; 0.200 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): 119 ; 0.287 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.141 ; 0.200 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): 1923 ; 0.575 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3068 ; 0.952 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1582 ; 1.349 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1422 ; 2.164 ; 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): 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 : 14 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 4 A 18 REMARK 3 ORIGIN FOR THE GROUP (A): 73.8331 -2.4647 17.3542 REMARK 3 T TENSOR REMARK 3 T11: 0.0449 T22: 0.0728 REMARK 3 T33: -0.1063 T12: -0.0330 REMARK 3 T13: 0.0592 T23: -0.0064 REMARK 3 L TENSOR REMARK 3 L11: 8.6670 L22: 6.6780 REMARK 3 L33: 3.3020 L12: 3.4603 REMARK 3 L13: -2.6776 L23: 2.5514 REMARK 3 S TENSOR REMARK 3 S11: -0.2523 S12: -0.7722 S13: -0.1307 REMARK 3 S21: 0.2378 S22: -0.0896 S23: 0.2546 REMARK 3 S31: 0.5666 S32: 0.0813 S33: 0.3419 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 19 A 44 REMARK 3 ORIGIN FOR THE GROUP (A): 86.2148 4.2778 9.7837 REMARK 3 T TENSOR REMARK 3 T11: 0.0130 T22: 0.0458 REMARK 3 T33: 0.0336 T12: -0.0500 REMARK 3 T13: 0.0378 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 1.1805 L22: 2.1150 REMARK 3 L33: 3.3190 L12: 1.1233 REMARK 3 L13: 0.6708 L23: -0.3900 REMARK 3 S TENSOR REMARK 3 S11: -0.0525 S12: 0.1339 S13: 0.0784 REMARK 3 S21: 0.2183 S22: -0.1451 S23: -0.1376 REMARK 3 S31: -0.2454 S32: 0.4656 S33: 0.1976 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 45 A 83 REMARK 3 ORIGIN FOR THE GROUP (A): 84.9069 -0.3825 13.2066 REMARK 3 T TENSOR REMARK 3 T11: 0.0269 T22: 0.0354 REMARK 3 T33: 0.0491 T12: -0.0343 REMARK 3 T13: 0.0271 T23: 0.0374 REMARK 3 L TENSOR REMARK 3 L11: 3.5663 L22: 1.8917 REMARK 3 L33: 2.3569 L12: 0.4712 REMARK 3 L13: 1.0895 L23: -0.6481 REMARK 3 S TENSOR REMARK 3 S11: 0.0693 S12: -0.2361 S13: -0.1097 REMARK 3 S21: -0.0193 S22: -0.1479 S23: -0.0406 REMARK 3 S31: 0.0607 S32: 0.2441 S33: 0.0786 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 84 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): 80.2023 -4.8983 16.8886 REMARK 3 T TENSOR REMARK 3 T11: 0.0151 T22: 0.0420 REMARK 3 T33: -0.0035 T12: -0.0481 REMARK 3 T13: -0.0186 T23: 0.0611 REMARK 3 L TENSOR REMARK 3 L11: 7.1040 L22: 1.6149 REMARK 3 L33: 0.9147 L12: 2.2942 REMARK 3 L13: 1.0843 L23: 1.1594 REMARK 3 S TENSOR REMARK 3 S11: 0.1625 S12: 0.0047 S13: -0.2980 REMARK 3 S21: 0.1899 S22: 0.0247 S23: -0.2195 REMARK 3 S31: 0.2732 S32: 0.1078 S33: -0.1872 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 : B 4 B 16 REMARK 3 ORIGIN FOR THE GROUP (A): 75.4133 39.4210 15.8359 REMARK 3 T TENSOR REMARK 3 T11: -0.0832 T22: 0.0605 REMARK 3 T33: -0.0085 T12: -0.0265 REMARK 3 T13: 0.0662 T23: 0.0190 REMARK 3 L TENSOR REMARK 3 L11: 3.6462 L22: 8.5600 REMARK 3 L33: 5.8962 L12: -4.8470 REMARK 3 L13: -1.0832 L23: -0.9134 REMARK 3 S TENSOR REMARK 3 S11: 0.1502 S12: 0.2371 S13: 0.4398 REMARK 3 S21: -0.1746 S22: 0.2824 S23: -0.0063 REMARK 3 S31: -0.2418 S32: 0.8693 S33: -0.4327 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 : B 17 B 52 REMARK 3 ORIGIN FOR THE GROUP (A): 70.3020 34.4132 29.3559 REMARK 3 T TENSOR REMARK 3 T11: 0.0500 T22: 0.0311 REMARK 3 T33: -0.0160 T12: -0.0127 REMARK 3 T13: 0.0212 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 3.0269 L22: 2.1535 REMARK 3 L33: 1.1140 L12: 0.0854 REMARK 3 L13: 0.7654 L23: -0.9387 REMARK 3 S TENSOR REMARK 3 S11: 0.0848 S12: -0.3117 S13: -0.0325 REMARK 3 S21: 0.2817 S22: -0.1554 S23: 0.0119 REMARK 3 S31: 0.0074 S32: 0.0086 S33: 0.0706 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 : B 53 B 84 REMARK 3 ORIGIN FOR THE GROUP (A): 73.8426 34.2315 25.9890 REMARK 3 T TENSOR REMARK 3 T11: 0.0462 T22: 0.0453 REMARK 3 T33: 0.0296 T12: -0.0161 REMARK 3 T13: 0.0264 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 4.6564 L22: 1.0727 REMARK 3 L33: 3.5234 L12: -0.6138 REMARK 3 L13: -0.5254 L23: -0.0160 REMARK 3 S TENSOR REMARK 3 S11: 0.0032 S12: -0.0300 S13: -0.1845 REMARK 3 S21: 0.0174 S22: -0.0987 S23: 0.0124 REMARK 3 S31: 0.1220 S32: 0.2629 S33: 0.0954 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 85 B 97 REMARK 3 ORIGIN FOR THE GROUP (A): 75.5368 41.2149 22.0817 REMARK 3 T TENSOR REMARK 3 T11: -0.0472 T22: 0.0108 REMARK 3 T33: 0.0313 T12: -0.0455 REMARK 3 T13: 0.0135 T23: 0.0814 REMARK 3 L TENSOR REMARK 3 L11: 2.4471 L22: 3.0547 REMARK 3 L33: 13.3101 L12: -2.7242 REMARK 3 L13: 4.4348 L23: -4.5963 REMARK 3 S TENSOR REMARK 3 S11: -0.1423 S12: 0.1535 S13: 0.3975 REMARK 3 S21: 0.1727 S22: -0.3799 S23: -0.3324 REMARK 3 S31: -0.0600 S32: 0.4694 S33: 0.5223 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 2 C 34 REMARK 3 ORIGIN FOR THE GROUP (A): 64.5480 11.3404 31.4043 REMARK 3 T TENSOR REMARK 3 T11: 0.0382 T22: 0.0067 REMARK 3 T33: 0.0480 T12: -0.0122 REMARK 3 T13: 0.0487 T23: -0.0177 REMARK 3 L TENSOR REMARK 3 L11: 3.5826 L22: 0.8914 REMARK 3 L33: 2.3699 L12: 0.4070 REMARK 3 L13: -0.3101 L23: 0.5733 REMARK 3 S TENSOR REMARK 3 S11: -0.0727 S12: 0.0539 S13: -0.1295 REMARK 3 S21: 0.0935 S22: 0.1874 S23: 0.0696 REMARK 3 S31: -0.0274 S32: 0.2909 S33: -0.1148 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 35 C 51 REMARK 3 ORIGIN FOR THE GROUP (A): 65.4027 2.4468 44.3177 REMARK 3 T TENSOR REMARK 3 T11: 0.0152 T22: -0.0425 REMARK 3 T33: -0.0159 T12: -0.0110 REMARK 3 T13: -0.0527 T23: 0.0957 REMARK 3 L TENSOR REMARK 3 L11: 13.9409 L22: 5.7097 REMARK 3 L33: 14.7738 L12: -0.6953 REMARK 3 L13: -9.1153 L23: 5.3869 REMARK 3 S TENSOR REMARK 3 S11: -0.1249 S12: -1.4439 S13: -0.7562 REMARK 3 S21: 0.8998 S22: -0.1212 S23: -0.5399 REMARK 3 S31: 0.4403 S32: 0.6060 S33: 0.2461 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 52 C 97 REMARK 3 ORIGIN FOR THE GROUP (A): 66.5904 10.4718 36.6090 REMARK 3 T TENSOR REMARK 3 T11: 0.0141 T22: 0.0166 REMARK 3 T33: 0.0265 T12: -0.0056 REMARK 3 T13: 0.0007 T23: -0.0437 REMARK 3 L TENSOR REMARK 3 L11: 1.3864 L22: 2.6175 REMARK 3 L33: 2.6795 L12: 0.7798 REMARK 3 L13: -1.9053 L23: -0.7067 REMARK 3 S TENSOR REMARK 3 S11: 0.0339 S12: -0.2223 S13: 0.0507 REMARK 3 S21: -0.0430 S22: 0.0442 S23: -0.1954 REMARK 3 S31: 0.0873 S32: 0.2002 S33: -0.0781 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 2 D 39 REMARK 3 ORIGIN FOR THE GROUP (A): 87.6493 26.1461 4.3323 REMARK 3 T TENSOR REMARK 3 T11: 0.0442 T22: 0.0206 REMARK 3 T33: 0.0036 T12: 0.0238 REMARK 3 T13: 0.0401 T23: 0.0247 REMARK 3 L TENSOR REMARK 3 L11: 1.7822 L22: 4.5705 REMARK 3 L33: 3.4747 L12: -0.7832 REMARK 3 L13: 0.9989 L23: 0.9892 REMARK 3 S TENSOR REMARK 3 S11: -0.0845 S12: -0.0398 S13: 0.0215 REMARK 3 S21: -0.1494 S22: 0.1456 S23: -0.2328 REMARK 3 S31: -0.1672 S32: 0.0398 S33: -0.0612 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 40 D 52 REMARK 3 ORIGIN FOR THE GROUP (A): 102.6511 32.9312 0.8888 REMARK 3 T TENSOR REMARK 3 T11: -0.0517 T22: 0.1753 REMARK 3 T33: 0.0129 T12: -0.1028 REMARK 3 T13: -0.0517 T23: 0.1106 REMARK 3 L TENSOR REMARK 3 L11: 6.7245 L22: 2.7264 REMARK 3 L33: 6.5643 L12: 1.2447 REMARK 3 L13: 0.0233 L23: 0.7255 REMARK 3 S TENSOR REMARK 3 S11: 0.2785 S12: -0.6226 S13: 0.1428 REMARK 3 S21: 0.7745 S22: -0.5263 S23: -1.5490 REMARK 3 S31: -0.8691 S32: 1.2828 S33: 0.2478 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 53 D 97 REMARK 3 ORIGIN FOR THE GROUP (A): 92.5256 25.5171 4.7586 REMARK 3 T TENSOR REMARK 3 T11: 0.0180 T22: 0.0204 REMARK 3 T33: 0.0074 T12: 0.0460 REMARK 3 T13: 0.0065 T23: -0.0132 REMARK 3 L TENSOR REMARK 3 L11: 1.3467 L22: 2.4961 REMARK 3 L33: 3.7338 L12: 0.4946 REMARK 3 L13: -2.1639 L23: -0.0241 REMARK 3 S TENSOR REMARK 3 S11: -0.0489 S12: -0.0980 S13: 0.1461 REMARK 3 S21: 0.2578 S22: 0.1704 S23: 0.0190 REMARK 3 S31: 0.2395 S32: 0.2324 S33: -0.1216 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 3DH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000048029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16347 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.32500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 1PY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M AMMONIUM SULFATE, PHOSPHATE REMARK 280 BUFFER PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 54.09600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.32400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.09600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.32400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ALA A 1 REMARK 465 ASP A 2 REMARK 465 PRO A 3 REMARK 465 ALA B 1 REMARK 465 ASP B 2 REMARK 465 PRO B 3 REMARK 465 ALA C 1 REMARK 465 ALA D 1 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 N ASN B 33 O3 BGC B 99 1.41 REMARK 500 NH2 ARG C 70 O4 BGC B 99 2.00 REMARK 500 OE2 GLU A 56 OH TYR A 87 2.09 REMARK 500 O ARG A 67 O HOH A 133 2.18 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 PRO A 47 131.51 -35.56 REMARK 500 ASN B 27 57.18 39.48 REMARK 500 ASN D 41 33.92 71.74 REMARK 500 ASP D 85 54.42 -145.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PY3 RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND REMARK 900 RELATED ID: 1PYL RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA2 WITHOUT LIGAND REMARK 900 RELATED ID: 3D4A RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA2 WITH 3'-GMP REMARK 900 RELATED ID: 3D5I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIBONUCLEASE SA2 WITH EXO-2',3'- REMARK 900 CYCLOPHOSPHOROTIOATE REMARK 900 RELATED ID: 1GMP RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA WITH 2'-GMP REMARK 900 RELATED ID: 3DGY RELATED DB: PDB REMARK 900 STRUCTURE OF RIBONUCLEASE SA2 WITH 2'-GMP DBREF 3DH2 A 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3DH2 B 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3DH2 C 1 97 UNP Q53752 Q53752_STRAU 67 163 DBREF 3DH2 D 1 97 UNP Q53752 Q53752_STRAU 67 163 SEQRES 1 A 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 A 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 A 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 A 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 A 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 A 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 A 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 A 97 GLU ILE ASP PRO ARG CYS SEQRES 1 B 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 B 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 B 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 B 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 B 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 B 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 B 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 B 97 GLU ILE ASP PRO ARG CYS SEQRES 1 C 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 C 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 C 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 C 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 C 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 C 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 C 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 C 97 GLU ILE ASP PRO ARG CYS SEQRES 1 D 97 ALA ASP PRO ALA LEU ALA ASP VAL CYS ARG THR LYS LEU SEQRES 2 D 97 PRO SER GLN ALA GLN ASP THR LEU ALA LEU ILE ALA LYS SEQRES 3 D 97 ASN GLY PRO TYR PRO TYR ASN ARG ASP GLY VAL VAL PHE SEQRES 4 D 97 GLU ASN ARG GLU SER ARG LEU PRO LYS LYS GLY ASN GLY SEQRES 5 D 97 TYR TYR HIS GLU PHE THR VAL VAL THR PRO GLY SER ASN SEQRES 6 D 97 ASP ARG GLY THR ARG ARG VAL VAL THR GLY GLY TYR GLY SEQRES 7 D 97 GLU GLN TYR TRP SER PRO ASP HIS TYR ALA THR PHE GLN SEQRES 8 D 97 GLU ILE ASP PRO ARG CYS HET BGC A 99 12 HET SO4 A 100 5 HET 3GP A 98 24 HET BGC B 99 12 HET 3GP B 98 24 HET BGC C 99 12 HET 3GP C 98 24 HET 3GP D 98 24 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETNAM 3GP GUANOSINE-3'-MONOPHOSPHATE FORMUL 5 BGC 3(C6 H12 O6) FORMUL 6 SO4 O4 S 2- FORMUL 7 3GP 4(C10 H14 N5 O8 P) FORMUL 13 HOH *125(H2 O) HELIX 1 1 THR A 11 LEU A 13 5 3 HELIX 2 2 PRO A 14 LYS A 26 1 13 HELIX 3 3 THR B 11 LEU B 13 5 3 HELIX 4 4 PRO B 14 LYS B 26 1 13 HELIX 5 5 THR C 11 LEU C 13 5 3 HELIX 6 6 PRO C 14 ASN C 27 1 14 HELIX 7 7 THR D 11 LEU D 13 5 3 HELIX 8 8 PRO D 14 LYS D 26 1 13 SHEET 1 A 6 ALA A 6 CYS A 9 0 SHEET 2 A 6 GLN A 91 ASP A 94 1 O ASP A 94 N VAL A 8 SHEET 3 A 6 GLN A 80 SER A 83 -1 N TRP A 82 O GLN A 91 SHEET 4 A 6 ARG A 71 THR A 74 -1 N VAL A 73 O TYR A 81 SHEET 5 A 6 TYR A 54 THR A 58 -1 N HIS A 55 O THR A 74 SHEET 6 A 6 VAL A 37 PHE A 39 -1 N VAL A 37 O GLU A 56 SHEET 1 B 5 ALA B 6 CYS B 9 0 SHEET 2 B 5 GLN B 91 ASP B 94 1 O ASP B 94 N VAL B 8 SHEET 3 B 5 GLN B 80 SER B 83 -1 N GLN B 80 O ILE B 93 SHEET 4 B 5 ARG B 70 THR B 74 -1 N VAL B 73 O TYR B 81 SHEET 5 B 5 HIS B 55 VAL B 59 -1 N VAL B 59 O ARG B 70 SHEET 1 C 6 ALA C 6 CYS C 9 0 SHEET 2 C 6 GLN C 91 ASP C 94 1 O GLU C 92 N ALA C 6 SHEET 3 C 6 GLN C 80 SER C 83 -1 N TRP C 82 O GLN C 91 SHEET 4 C 6 ARG C 71 THR C 74 -1 N VAL C 73 O TYR C 81 SHEET 5 C 6 HIS C 55 THR C 58 -1 N PHE C 57 O VAL C 72 SHEET 6 C 6 VAL C 37 VAL C 38 -1 N VAL C 37 O GLU C 56 SHEET 1 D 6 ALA D 6 CYS D 9 0 SHEET 2 D 6 GLN D 91 ASP D 94 1 O GLU D 92 N ALA D 6 SHEET 3 D 6 GLN D 80 SER D 83 -1 N TRP D 82 O GLN D 91 SHEET 4 D 6 ARG D 71 THR D 74 -1 N VAL D 73 O TYR D 81 SHEET 5 D 6 HIS D 55 THR D 58 -1 N PHE D 57 O VAL D 72 SHEET 6 D 6 VAL D 37 VAL D 38 -1 N VAL D 37 O GLU D 56 SSBOND 1 CYS A 9 CYS A 97 1555 1555 2.03 SSBOND 2 CYS B 9 CYS B 97 1555 1555 2.04 SSBOND 3 CYS C 9 CYS C 97 1555 1555 2.02 SSBOND 4 CYS D 9 CYS D 97 1555 1555 2.02 CISPEP 1 GLY A 28 PRO A 29 0 -0.30 CISPEP 2 GLY B 28 PRO B 29 0 -0.81 CISPEP 3 GLY C 28 PRO C 29 0 0.63 CISPEP 4 GLY D 28 PRO D 29 0 5.17 CRYST1 108.192 62.648 68.299 90.00 129.18 90.00 C 1 2 1 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 0.009243 0.000000 0.007532 0.00000 SCALE2 0.000000 0.015962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018888 0.00000 MASTER 580 0 8 8 23 0 0 6 0 0 0 32 END