HEADER OXIDOREDUCTASE 14-SEP-12 3VXJ TITLE DYE-DECOLORIZING PEROXIDASE (DYP) COMPLEX WITH 2,6-DIMETHOXYPHENOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: DYP; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 57-498; COMPND 5 SYNONYM: DYE-DECOLORIZING PEROXIDASE; COMPND 6 EC: 1.11.1.19; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BJERKANDERA ADUSTA; SOURCE 3 ORGANISM_TAXID: 5331; SOURCE 4 STRAIN: DEC 1; SOURCE 5 GENE: DYP; SOURCE 6 EXPRESSION_SYSTEM: ASPERGILLUS ORYZAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 5062; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M-2-3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTAEX3 KEYWDS DYP, DYE-DECOLORIZING PEROXIDASE, 2, 6-DIMETHOXYPHENOL, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.SUGANO,T.YOSHIDA,H.TSUGE REVDAT 4 08-NOV-23 3VXJ 1 HETSYN REVDAT 3 29-JUL-20 3VXJ 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 22-NOV-17 3VXJ 1 REMARK REVDAT 1 07-NOV-12 3VXJ 0 JRNL AUTH Y.SUGANO,T.YOSHIDA,H.TSUGE JRNL TITL DYE-DECOLORIZING PEROXIDASE (DYP) COMPLEX WITH JRNL TITL 2 2,6-DIMETHOXYPHENOL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 77869 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3880 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) : 1.39 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5206 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 281 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3331 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 83 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.75000 REMARK 3 B22 (A**2) : -0.85000 REMARK 3 B33 (A**2) : 0.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.38000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.063 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.547 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3508 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4798 ; 1.243 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 437 ; 5.857 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;38.008 ;24.908 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 494 ;10.558 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;22.833 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 515 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2788 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 5 A 18 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0707 -7.6032 28.2671 REMARK 3 T TENSOR REMARK 3 T11: 0.0551 T22: 0.0606 REMARK 3 T33: 0.0437 T12: -0.0115 REMARK 3 T13: -0.0229 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 1.6938 L22: 2.3171 REMARK 3 L33: 3.9965 L12: -0.2015 REMARK 3 L13: -0.7481 L23: -1.8618 REMARK 3 S TENSOR REMARK 3 S11: 0.0141 S12: -0.2047 S13: 0.0832 REMARK 3 S21: 0.3536 S22: 0.0147 S23: -0.0240 REMARK 3 S31: -0.3029 S32: 0.1056 S33: -0.0288 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 38 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0660 -13.3672 10.9918 REMARK 3 T TENSOR REMARK 3 T11: 0.0217 T22: 0.0749 REMARK 3 T33: 0.0575 T12: 0.0114 REMARK 3 T13: 0.0002 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 1.1277 L22: 1.9608 REMARK 3 L33: 0.9163 L12: 0.3748 REMARK 3 L13: 0.0724 L23: -0.4192 REMARK 3 S TENSOR REMARK 3 S11: 0.0190 S12: -0.0056 S13: 0.0246 REMARK 3 S21: -0.0445 S22: -0.0259 S23: 0.0004 REMARK 3 S31: 0.0208 S32: 0.0556 S33: 0.0069 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 39 A 54 REMARK 3 ORIGIN FOR THE GROUP (A): 20.7006 -15.7787 20.9823 REMARK 3 T TENSOR REMARK 3 T11: 0.0137 T22: 0.0996 REMARK 3 T33: 0.0574 T12: 0.0083 REMARK 3 T13: -0.0350 T23: 0.0251 REMARK 3 L TENSOR REMARK 3 L11: 0.5903 L22: 4.2959 REMARK 3 L33: 1.1421 L12: -0.4229 REMARK 3 L13: -0.7720 L23: 1.6541 REMARK 3 S TENSOR REMARK 3 S11: -0.0063 S12: -0.1335 S13: -0.0335 REMARK 3 S21: 0.1269 S22: 0.0176 S23: -0.2588 REMARK 3 S31: 0.0543 S32: 0.2080 S33: -0.0113 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 55 A 65 REMARK 3 ORIGIN FOR THE GROUP (A): 24.5975 -1.9622 24.7583 REMARK 3 T TENSOR REMARK 3 T11: 0.1219 T22: 0.1946 REMARK 3 T33: 0.1418 T12: -0.1768 REMARK 3 T13: -0.1212 T23: 0.0679 REMARK 3 L TENSOR REMARK 3 L11: 9.7892 L22: -0.4698 REMARK 3 L33: 30.4433 L12: 1.3457 REMARK 3 L13: -7.0118 L23: 3.4940 REMARK 3 S TENSOR REMARK 3 S11: -0.1541 S12: -0.6276 S13: 1.1936 REMARK 3 S21: 0.2953 S22: 0.1029 S23: 0.2547 REMARK 3 S31: -0.1365 S32: 2.3960 S33: 0.0512 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 66 A 89 REMARK 3 ORIGIN FOR THE GROUP (A): 4.7920 -18.9418 16.5500 REMARK 3 T TENSOR REMARK 3 T11: 0.0351 T22: 0.0405 REMARK 3 T33: 0.0563 T12: 0.0034 REMARK 3 T13: -0.0069 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.7337 L22: 0.2534 REMARK 3 L33: 0.6028 L12: -0.0271 REMARK 3 L13: -0.4389 L23: -0.1604 REMARK 3 S TENSOR REMARK 3 S11: -0.0309 S12: -0.0004 S13: -0.0882 REMARK 3 S21: 0.0282 S22: -0.0114 S23: 0.0126 REMARK 3 S31: 0.0717 S32: -0.0034 S33: 0.0423 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 90 A 115 REMARK 3 ORIGIN FOR THE GROUP (A): -3.0658 -10.3617 4.0217 REMARK 3 T TENSOR REMARK 3 T11: 0.0411 T22: 0.0510 REMARK 3 T33: 0.0394 T12: 0.0025 REMARK 3 T13: -0.0156 T23: -0.0190 REMARK 3 L TENSOR REMARK 3 L11: 0.8257 L22: 1.4519 REMARK 3 L33: 0.4407 L12: -0.3495 REMARK 3 L13: 0.0522 L23: 0.0587 REMARK 3 S TENSOR REMARK 3 S11: 0.0473 S12: 0.0870 S13: -0.0127 REMARK 3 S21: -0.1694 S22: -0.0523 S23: 0.0356 REMARK 3 S31: -0.0026 S32: -0.0389 S33: 0.0050 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 116 A 161 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5978 -8.1977 8.3479 REMARK 3 T TENSOR REMARK 3 T11: 0.0156 T22: 0.0618 REMARK 3 T33: 0.0559 T12: -0.0006 REMARK 3 T13: -0.0087 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.5633 L22: 0.7628 REMARK 3 L33: 0.3316 L12: 0.1017 REMARK 3 L13: -0.0864 L23: -0.0121 REMARK 3 S TENSOR REMARK 3 S11: 0.0002 S12: 0.0208 S13: 0.0245 REMARK 3 S21: -0.0498 S22: -0.0058 S23: -0.0763 REMARK 3 S31: 0.0220 S32: 0.0520 S33: 0.0055 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 : A 162 A 188 REMARK 3 ORIGIN FOR THE GROUP (A): 7.3579 7.1829 22.4743 REMARK 3 T TENSOR REMARK 3 T11: 0.0360 T22: 0.0841 REMARK 3 T33: 0.0576 T12: -0.0014 REMARK 3 T13: -0.0296 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.5508 L22: 1.2638 REMARK 3 L33: 0.7553 L12: 0.2580 REMARK 3 L13: -0.6966 L23: 0.1506 REMARK 3 S TENSOR REMARK 3 S11: 0.0075 S12: -0.1722 S13: -0.0755 REMARK 3 S21: 0.2155 S22: -0.0808 S23: -0.1590 REMARK 3 S31: 0.0827 S32: 0.1870 S33: 0.0733 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 : A 189 A 218 REMARK 3 ORIGIN FOR THE GROUP (A): 1.0786 -10.6121 28.1267 REMARK 3 T TENSOR REMARK 3 T11: 0.0387 T22: 0.0469 REMARK 3 T33: 0.0350 T12: -0.0015 REMARK 3 T13: -0.0064 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.6953 L22: 1.4889 REMARK 3 L33: 0.4997 L12: 0.3692 REMARK 3 L13: -0.0307 L23: -0.3369 REMARK 3 S TENSOR REMARK 3 S11: -0.0109 S12: -0.0748 S13: 0.0178 REMARK 3 S21: 0.1447 S22: 0.0129 S23: 0.0294 REMARK 3 S31: -0.0334 S32: 0.0107 S33: -0.0019 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 : A 219 A 233 REMARK 3 ORIGIN FOR THE GROUP (A): 2.1640 6.3858 2.3655 REMARK 3 T TENSOR REMARK 3 T11: 0.0538 T22: 0.0577 REMARK 3 T33: 0.0236 T12: 0.0097 REMARK 3 T13: -0.0068 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.3263 L22: 2.7515 REMARK 3 L33: 0.8033 L12: -0.3356 REMARK 3 L13: 0.0649 L23: -1.3249 REMARK 3 S TENSOR REMARK 3 S11: 0.0425 S12: 0.0811 S13: 0.0046 REMARK 3 S21: -0.1679 S22: -0.0748 S23: -0.0232 REMARK 3 S31: -0.0119 S32: 0.0097 S33: 0.0322 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 : A 234 A 315 REMARK 3 ORIGIN FOR THE GROUP (A): -2.7128 19.5559 16.2544 REMARK 3 T TENSOR REMARK 3 T11: 0.0287 T22: 0.0393 REMARK 3 T33: 0.0349 T12: -0.0066 REMARK 3 T13: -0.0051 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.3426 L22: 0.9311 REMARK 3 L33: 0.5743 L12: -0.1544 REMARK 3 L13: -0.0338 L23: -0.2352 REMARK 3 S TENSOR REMARK 3 S11: 0.0084 S12: 0.0070 S13: 0.0415 REMARK 3 S21: 0.0259 S22: -0.0260 S23: -0.0310 REMARK 3 S31: -0.0798 S32: 0.0514 S33: 0.0177 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 : A 316 A 381 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7400 3.0661 12.4348 REMARK 3 T TENSOR REMARK 3 T11: 0.0375 T22: 0.0478 REMARK 3 T33: 0.0448 T12: -0.0021 REMARK 3 T13: -0.0130 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 0.6314 L22: 0.8428 REMARK 3 L33: 0.3510 L12: -0.2236 REMARK 3 L13: 0.0530 L23: -0.0004 REMARK 3 S TENSOR REMARK 3 S11: 0.0152 S12: 0.0468 S13: 0.0306 REMARK 3 S21: -0.0414 S22: -0.0174 S23: -0.0012 REMARK 3 S31: -0.0446 S32: 0.0225 S33: 0.0022 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 : A 382 A 420 REMARK 3 ORIGIN FOR THE GROUP (A): -12.2044 12.8592 8.2171 REMARK 3 T TENSOR REMARK 3 T11: 0.0209 T22: 0.0468 REMARK 3 T33: 0.0512 T12: 0.0028 REMARK 3 T13: -0.0205 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.6699 L22: 1.0097 REMARK 3 L33: 0.6371 L12: -0.4770 REMARK 3 L13: -0.2668 L23: 0.3771 REMARK 3 S TENSOR REMARK 3 S11: 0.0286 S12: 0.0457 S13: -0.0453 REMARK 3 S21: -0.1047 S22: -0.0400 S23: 0.1170 REMARK 3 S31: -0.0265 S32: -0.0485 S33: 0.0114 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 : A 421 A 442 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2444 -14.8769 16.4182 REMARK 3 T TENSOR REMARK 3 T11: 0.0306 T22: 0.0540 REMARK 3 T33: 0.0598 T12: 0.0018 REMARK 3 T13: -0.0017 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 0.6218 L22: 1.0345 REMARK 3 L33: 1.2985 L12: -0.2203 REMARK 3 L13: 0.3035 L23: -0.5706 REMARK 3 S TENSOR REMARK 3 S11: 0.0226 S12: -0.0139 S13: -0.0714 REMARK 3 S21: -0.0234 S22: -0.0367 S23: -0.0471 REMARK 3 S31: 0.0895 S32: 0.0738 S33: 0.0141 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3VXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000095624. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR, REMARK 200 LIQUID NITROGEN COOLING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77992 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3AFV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, PH 6.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 48.17200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 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 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 ASN A 2 REMARK 465 ASP A 3 REMARK 465 THR A 4 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 FE HEM A 501 O HOH A 863 1.99 REMARK 500 NE2 HIS A 308 FE HEM A 501 2.17 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 ASP A 292 10.63 -145.98 REMARK 500 THR A 296 34.78 -153.81 REMARK 500 ARG A 315 -127.18 48.02 REMARK 500 TRP A 374 -70.96 -110.48 REMARK 500 THR A 439 -61.58 -120.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VXI RELATED DB: PDB DBREF 3VXJ A 1 442 UNP Q8WZK8 Q8WZK8_9APHY 57 498 SEQRES 1 A 442 ALA ASN ASP THR ILE LEU PRO LEU ASN ASN ILE GLN GLY SEQRES 2 A 442 ASP ILE LEU VAL GLY MET LYS LYS GLN LYS GLU ARG PHE SEQRES 3 A 442 VAL PHE PHE GLN VAL ASN ASP ALA THR SER PHE LYS THR SEQRES 4 A 442 ALA LEU LYS THR TYR VAL PRO GLU ARG ILE THR SER ALA SEQRES 5 A 442 ALA ILE LEU ILE SER ASP PRO SER GLN GLN PRO LEU ALA SEQRES 6 A 442 PHE VAL ASN LEU GLY PHE SER ASN THR GLY LEU GLN ALA SEQRES 7 A 442 LEU GLY ILE THR ASP ASP LEU GLY ASP ALA GLN PHE PRO SEQRES 8 A 442 ASP GLY GLN PHE ALA ASP ALA ALA ASN LEU GLY ASP ASP SEQRES 9 A 442 LEU SER GLN TRP VAL ALA PRO PHE THR GLY THR THR ILE SEQRES 10 A 442 HIS GLY VAL PHE LEU ILE GLY SER ASP GLN ASP ASP PHE SEQRES 11 A 442 LEU ASP GLN PHE THR ASP ASP ILE SER SER THR PHE GLY SEQRES 12 A 442 SER SER ILE THR GLN VAL GLN ALA LEU SER GLY SER ALA SEQRES 13 A 442 ARG PRO GLY ASP GLN ALA GLY HIS GLU HIS PHE GLY PHE SEQRES 14 A 442 LEU ASP GLY ILE SER GLN PRO SER VAL THR GLY TRP GLU SEQRES 15 A 442 THR THR VAL PHE PRO GLY GLN ALA VAL VAL PRO PRO GLY SEQRES 16 A 442 ILE ILE LEU THR GLY ARG ASP GLY ASP THR GLY THR ARG SEQRES 17 A 442 PRO SER TRP ALA LEU ASP GLY SER PHE MET ALA PHE ARG SEQRES 18 A 442 HIS PHE GLN GLN LYS VAL PRO GLU PHE ASN ALA TYR THR SEQRES 19 A 442 LEU ALA ASN ALA ILE PRO ALA ASN SER ALA GLY ASN LEU SEQRES 20 A 442 THR GLN GLN GLU GLY ALA GLU PHE LEU GLY ALA ARG MET SEQRES 21 A 442 PHE GLY ARG TRP LYS SER GLY ALA PRO ILE ASP LEU ALA SEQRES 22 A 442 PRO THR ALA ASP ASP PRO ALA LEU GLY ALA ASP PRO GLN SEQRES 23 A 442 ARG ASN ASN ASN PHE ASP TYR SER ASP THR LEU THR ASP SEQRES 24 A 442 GLU THR ARG CYS PRO PHE GLY ALA HIS VAL ARG LYS THR SEQRES 25 A 442 ASN PRO ARG GLN ASP LEU GLY GLY PRO VAL ASP THR PHE SEQRES 26 A 442 HIS ALA MET ARG SER SER ILE PRO TYR GLY PRO GLU THR SEQRES 27 A 442 SER ASP ALA GLU LEU ALA SER GLY VAL THR ALA GLN ASP SEQRES 28 A 442 ARG GLY LEU LEU PHE VAL GLU TYR GLN SER ILE ILE GLY SEQRES 29 A 442 ASN GLY PHE ARG PHE GLN GLN ILE ASN TRP ALA ASN ASN SEQRES 30 A 442 ALA ASN PHE PRO PHE SER LYS PRO ILE THR PRO GLY ILE SEQRES 31 A 442 GLU PRO ILE ILE GLY GLN THR THR PRO ARG THR VAL GLY SEQRES 32 A 442 GLY LEU ASP PRO LEU ASN GLN ASN GLU THR PHE THR VAL SEQRES 33 A 442 PRO LEU PHE VAL ILE PRO LYS GLY GLY GLU TYR PHE PHE SEQRES 34 A 442 LEU PRO SER ILE SER ALA LEU THR ALA THR ILE ALA ALA MODRES 3VXJ ASN A 246 ASN GLYCOSYLATION SITE HET HEM A 501 43 HET NAG A 502 14 HET 3DM A 503 11 HET 3DM A 504 11 HET DMS A 505 4 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM 3DM 2,6-DIMETHOXYPHENOL HETNAM DMS DIMETHYL SULFOXIDE HETSYN HEM HEME 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 2 HEM C34 H32 FE N4 O4 FORMUL 3 NAG C8 H15 N O6 FORMUL 4 3DM 2(C8 H10 O3) FORMUL 6 DMS C2 H6 O S FORMUL 7 HOH *165(H2 O) HELIX 1 1 GLN A 12 VAL A 17 1 6 HELIX 2 2 ASP A 33 ILE A 49 1 17 HELIX 3 3 SER A 51 ILE A 56 1 6 HELIX 4 4 ASP A 58 GLN A 62 5 5 HELIX 5 5 SER A 72 LEU A 79 1 8 HELIX 6 6 GLN A 89 GLY A 93 5 5 HELIX 7 7 GLN A 94 ALA A 96 5 3 HELIX 8 8 ASP A 97 GLY A 102 1 6 HELIX 9 9 ASP A 104 TRP A 108 5 5 HELIX 10 10 GLN A 127 GLY A 143 1 17 HELIX 11 11 PRO A 158 ALA A 162 5 5 HELIX 12 12 PRO A 193 ILE A 197 5 5 HELIX 13 13 PRO A 209 LEU A 213 5 5 HELIX 14 14 LYS A 226 ASN A 237 1 12 HELIX 15 15 THR A 248 GLY A 262 1 15 HELIX 16 16 ASP A 278 ALA A 283 1 6 HELIX 17 17 ALA A 307 ASN A 313 1 7 HELIX 18 18 PRO A 314 GLY A 319 5 6 HELIX 19 19 SER A 339 GLY A 346 1 8 HELIX 20 20 ILE A 362 ASN A 365 5 4 HELIX 21 21 GLY A 366 ILE A 372 1 7 HELIX 22 22 SER A 432 THR A 439 1 8 SHEET 1 A 4 ALA A 65 PHE A 71 0 SHEET 2 A 4 GLY A 119 SER A 125 -1 O LEU A 122 N ASN A 68 SHEET 3 A 4 LYS A 23 VAL A 31 -1 N VAL A 27 O PHE A 121 SHEET 4 A 4 ILE A 146 SER A 155 -1 O GLY A 154 N GLU A 24 SHEET 1 B 2 SER A 177 VAL A 178 0 SHEET 2 B 2 VAL A 191 VAL A 192 1 O VAL A 192 N SER A 177 SHEET 1 C 3 MET A 328 ARG A 329 0 SHEET 2 C 3 GLY A 353 GLN A 360 -1 O TYR A 359 N MET A 328 SHEET 3 C 3 ILE A 332 TYR A 334 -1 N ILE A 332 O LEU A 355 SHEET 1 D 4 MET A 328 ARG A 329 0 SHEET 2 D 4 GLY A 353 GLN A 360 -1 O TYR A 359 N MET A 328 SHEET 3 D 4 SER A 216 GLN A 225 -1 N ALA A 219 O GLU A 358 SHEET 4 D 4 VAL A 420 LEU A 430 -1 O LYS A 423 N HIS A 222 SHEET 1 E 2 ALA A 241 ASN A 242 0 SHEET 2 E 2 GLY A 245 ASN A 246 -1 O GLY A 245 N ASN A 242 SHEET 1 F 2 THR A 401 GLY A 403 0 SHEET 2 F 2 THR A 413 THR A 415 -1 O PHE A 414 N VAL A 402 LINK ND2 ASN A 246 C1 NAG A 502 1555 1555 1.44 CISPEP 1 ALA A 110 PRO A 111 0 3.41 CISPEP 2 PHE A 380 PRO A 381 0 2.04 CISPEP 3 THR A 398 PRO A 399 0 -0.35 CRYST1 45.167 96.344 49.778 90.00 106.71 90.00 P 1 21 1 2 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 0.022140 0.000000 0.006644 0.00000 SCALE2 0.000000 0.010379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020974 0.00000