HEADER HYDROLASE 26-SEP-16 5GZ5 TITLE CRYSTAL STRUCTURE OF SNAKE VENOM PHOSPHODIESTERASE (PDE) FROM TAIWAN TITLE 2 COBRA (NAJA ATRA ATRA) IN COMPLEX WITH AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SNAKE VENOM PHOSPHODIESTERASE (PDE); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA ATRA; SOURCE 3 ORGANISM_TAXID: 8656 KEYWDS PHSOPHODIESTERASE, ENPP, ZINC, CALCIUM, N-GLYCAN, AMP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.C.LIN,B.S.WU,W.G.WU REVDAT 3 08-NOV-23 5GZ5 1 HETSYN LINK REVDAT 2 29-JUL-20 5GZ5 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE ATOM REVDAT 1 27-SEP-17 5GZ5 0 JRNL AUTH C.C.LIN,B.S.WU,W.G.WU JRNL TITL CRYSTAL STRUCTURE OF SNAKE VENOM PHOSPHODIESTERASE (PDE) JRNL TITL 2 FROM TAIWAN COBRA (NAJA ATRA ATRA) IN COMPLEX WITH AMP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 58941 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 2923 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.8789 - 5.7593 0.96 2806 153 0.2239 0.2264 REMARK 3 2 5.7593 - 4.5779 0.98 2720 155 0.1673 0.1894 REMARK 3 3 4.5779 - 4.0012 1.00 2725 158 0.1426 0.1943 REMARK 3 4 4.0012 - 3.6362 0.99 2705 136 0.1496 0.1662 REMARK 3 5 3.6362 - 3.3760 0.99 2720 138 0.1603 0.1995 REMARK 3 6 3.3760 - 3.1773 1.00 2698 137 0.1637 0.2081 REMARK 3 7 3.1773 - 3.0184 1.00 2728 112 0.1710 0.1814 REMARK 3 8 3.0184 - 2.8871 1.00 2672 157 0.1814 0.2470 REMARK 3 9 2.8871 - 2.7761 1.00 2651 141 0.1819 0.2344 REMARK 3 10 2.7761 - 2.6804 1.00 2690 120 0.1879 0.2363 REMARK 3 11 2.6804 - 2.5966 1.00 2701 128 0.1834 0.2669 REMARK 3 12 2.5966 - 2.5224 0.99 2639 149 0.1890 0.2613 REMARK 3 13 2.5224 - 2.4561 0.99 2673 134 0.1856 0.2574 REMARK 3 14 2.4561 - 2.3962 0.99 2666 110 0.1860 0.2464 REMARK 3 15 2.3962 - 2.3417 0.99 2640 128 0.1916 0.2320 REMARK 3 16 2.3417 - 2.2919 0.99 2672 145 0.1885 0.2524 REMARK 3 17 2.2919 - 2.2461 0.99 2637 142 0.1991 0.2429 REMARK 3 18 2.2461 - 2.2037 0.99 2626 143 0.1932 0.2301 REMARK 3 19 2.2037 - 2.1644 0.99 2625 139 0.1989 0.2468 REMARK 3 20 2.1644 - 2.1277 0.98 2611 155 0.2211 0.2745 REMARK 3 21 2.1277 - 2.0934 0.91 2413 143 0.2215 0.2680 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 6605 REMARK 3 ANGLE : 1.290 9001 REMARK 3 CHIRALITY : 0.064 1004 REMARK 3 PLANARITY : 0.008 1131 REMARK 3 DIHEDRAL : 17.229 3994 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 468 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.7892 -5.9684 -45.0643 REMARK 3 T TENSOR REMARK 3 T11: 0.1673 T22: 0.3651 REMARK 3 T33: 0.1515 T12: -0.0084 REMARK 3 T13: -0.0412 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 2.1080 L22: 1.6951 REMARK 3 L33: 1.9782 L12: 0.4828 REMARK 3 L13: 0.0852 L23: 0.4563 REMARK 3 S TENSOR REMARK 3 S11: -0.2095 S12: 0.6750 S13: -0.0376 REMARK 3 S21: -0.2850 S22: 0.1997 S23: 0.0604 REMARK 3 S31: 0.1352 S32: 0.2479 S33: 0.0397 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 469 THROUGH 852 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.1508 12.5536 -13.9869 REMARK 3 T TENSOR REMARK 3 T11: 0.2035 T22: 0.1322 REMARK 3 T33: 0.2966 T12: 0.0318 REMARK 3 T13: 0.0661 T23: 0.0331 REMARK 3 L TENSOR REMARK 3 L11: 0.9548 L22: 1.2351 REMARK 3 L33: 1.9763 L12: -0.0549 REMARK 3 L13: -0.5337 L23: 0.7040 REMARK 3 S TENSOR REMARK 3 S11: -0.0170 S12: -0.0840 S13: 0.2293 REMARK 3 S21: 0.2596 S22: 0.0770 S23: 0.2497 REMARK 3 S31: -0.0447 S32: 0.0945 S33: -0.0727 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5GZ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59141 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 5GZ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE PH6.5, 0.2M ZINC REMARK 280 ACETATE, 20% PEG 3000, 1MM AMP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 85.60350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.80600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 85.60350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.80600 REMARK 290 SMTRY3 4 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 TOTAL BURIED SURFACE AREA: 3050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 16.0 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 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 LEU A 24 REMARK 465 LYS A 25 REMARK 465 GLN A 26 REMARK 465 SER A 27 REMARK 465 LYS A 28 REMARK 465 GLN A 29 REMARK 465 PRO A 30 REMARK 465 LEU A 31 REMARK 465 GLU A 32 REMARK 465 SER A 33 REMARK 465 CYS A 34 REMARK 465 ARG A 35 REMARK 465 ASN A 36 REMARK 465 ARG A 37 REMARK 465 CYS A 38 REMARK 465 ASN A 39 REMARK 465 GLU A 40 REMARK 465 THR A 41 REMARK 465 PHE A 42 REMARK 465 SER A 43 REMARK 465 GLU A 44 REMARK 465 GLU A 45 REMARK 465 LEU A 46 REMARK 465 SER A 47 REMARK 465 TYR A 48 REMARK 465 CYS A 49 REMARK 465 SER A 50 REMARK 465 CYS A 51 REMARK 465 ASP A 52 REMARK 465 ASN A 53 REMARK 465 LYS A 54 REMARK 465 CYS A 55 REMARK 465 THR A 56 REMARK 465 GLU A 57 REMARK 465 ARG A 58 REMARK 465 LYS A 59 REMARK 465 ALA A 60 REMARK 465 CYS A 61 REMARK 465 CYS A 62 REMARK 465 TRP A 63 REMARK 465 ASP A 64 REMARK 465 SER A 126 REMARK 465 SER A 127 REMARK 465 SER A 128 REMARK 465 ALA A 129 REMARK 465 VAL A 628 REMARK 465 LYS A 629 REMARK 465 PRO A 630 REMARK 465 THR A 631 REMARK 465 SER A 632 REMARK 465 ALA A 633 REMARK 465 PRO A 634 REMARK 465 ASN A 853 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 1105 O HOH A 1702 1.98 REMARK 500 O HOH A 1135 O HOH A 1628 2.05 REMARK 500 O HOH A 1637 O HOH A 1790 2.06 REMARK 500 O HOH A 1677 O HOH A 1756 2.08 REMARK 500 O HOH A 1102 O HOH A 1690 2.10 REMARK 500 O HOH A 1570 O HOH A 1615 2.10 REMARK 500 O HOH A 1651 O HOH A 1705 2.13 REMARK 500 ND2 ASN A 226 O HOH A 1101 2.14 REMARK 500 O HOH A 1217 O HOH A 1507 2.16 REMARK 500 O HOH A 1410 O HOH A 1468 2.16 REMARK 500 O2P AMP A 1016 O HOH A 1102 2.17 REMARK 500 O HOH A 1128 O HOH A 1429 2.17 REMARK 500 ND2 ASN A 512 O5 NAG B 1 2.17 REMARK 500 OG1 THR A 185 O3P AMP A 1016 2.19 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 CYS A 78 52.06 -90.48 REMARK 500 ASN A 79 156.23 -44.84 REMARK 500 GLU A 85 173.61 -56.71 REMARK 500 SER A 96 -149.37 -115.15 REMARK 500 ASP A 98 37.08 -82.89 REMARK 500 PRO A 133 -150.66 -92.94 REMARK 500 SER A 220 66.68 -119.48 REMARK 500 PHE A 250 128.42 73.51 REMARK 500 TRP A 251 134.14 -170.32 REMARK 500 VAL A 373 70.59 -112.96 REMARK 500 PRO A 424 128.15 -38.98 REMARK 500 ALA A 430 -36.71 -154.00 REMARK 500 GLN A 445 -2.76 81.75 REMARK 500 TYR A 456 58.39 -94.79 REMARK 500 ASP A 465 129.52 -34.98 REMARK 500 LYS A 485 53.98 37.80 REMARK 500 CYS A 556 85.85 -151.25 REMARK 500 SER A 626 154.55 73.34 REMARK 500 ALA A 637 -73.07 -94.87 REMARK 500 ASP A 661 81.61 -66.59 REMARK 500 TYR A 731 43.12 37.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 69 VAL A 70 148.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1885 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1886 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A1887 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A1888 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A1889 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A1890 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A1891 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A1892 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH A1893 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A1894 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A1895 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH A1896 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH A1897 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH A1898 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH A1899 DISTANCE = 7.33 ANGSTROMS REMARK 525 HOH A1900 DISTANCE = 7.43 ANGSTROMS REMARK 525 HOH A1901 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH A1902 DISTANCE = 7.86 ANGSTROMS REMARK 525 HOH A1903 DISTANCE = 8.33 ANGSTROMS REMARK 525 HOH A1904 DISTANCE = 8.57 ANGSTROMS REMARK 525 HOH A1905 DISTANCE = 8.66 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1014 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 147 OD1 REMARK 620 2 ASP A 147 OD2 53.5 REMARK 620 3 THR A 185 OG1 124.1 85.2 REMARK 620 4 ASP A 352 OD2 108.6 89.6 106.4 REMARK 620 5 HIS A 353 NE2 106.2 159.6 111.4 96.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1013 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 305 OD1 REMARK 620 2 ASP A 305 OD2 55.8 REMARK 620 3 HIS A 309 NE2 102.9 85.1 REMARK 620 4 HIS A 462 NE2 94.2 149.9 106.1 REMARK 620 5 AMP A1016 O1P 126.1 75.6 94.0 129.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1015 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 728 OD1 REMARK 620 2 ASN A 730 OD1 87.9 REMARK 620 3 ASP A 732 OD1 103.7 93.4 REMARK 620 4 HIS A 734 O 93.0 175.1 91.1 REMARK 620 5 ASP A 736 OD1 145.7 86.9 110.5 89.7 REMARK 620 6 ASP A 736 OD2 88.3 74.3 162.7 100.9 57.7 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GZ4 RELATED DB: PDB DBREF 5GZ5 A 24 853 PDB 5GZ5 5GZ5 24 853 SEQRES 1 A 830 LEU LYS GLN SER LYS GLN PRO LEU GLU SER CYS ARG ASN SEQRES 2 A 830 ARG CYS ASN GLU THR PHE SER GLU GLU LEU SER TYR CYS SEQRES 3 A 830 SER CYS ASP ASN LYS CYS THR GLU ARG LYS ALA CYS CYS SEQRES 4 A 830 TRP ASP TYR GLN ASP ILE CYS VAL LEU PRO THR GLN SER SEQRES 5 A 830 TRP SER CYS ASN LYS LEU ARG CYS GLY GLU LYS ARG MET SEQRES 6 A 830 ALA ASN VAL LEU CYS SER CYS SER GLU ASP CYS LEU THR SEQRES 7 A 830 LYS LYS ASP CYS CYS THR ASP TYR LYS SER ILE CYS LYS SEQRES 8 A 830 ARG GLU THR SER TRP LEU LYS ASP GLN CYS ALA SER SER SEQRES 9 A 830 SER ALA SER GLN CYS PRO GLU GLY PHE ASP GLN SER PRO SEQRES 10 A 830 LEU ILE LEU PHE SER MET ASP GLY PHE ARG ALA GLU TYR SEQRES 11 A 830 LEU GLU THR TRP ASP THR LEU MET PRO ASN ILE ASN LYS SEQRES 12 A 830 LEU LYS THR CYS GLY THR HIS ALA LYS TYR MET ARG ALA SEQRES 13 A 830 VAL TYR PRO THR LYS THR PHE VAL ASN HIS TYR THR ILE SEQRES 14 A 830 VAL THR GLY LEU TYR ALA GLU THR HIS GLY ILE ILE ASP SEQRES 15 A 830 ASN ASN MET TYR ASP VAL LYS LEU ASN GLN ASN PHE SER SEQRES 16 A 830 LEU SER GLY SER ASN MET ARG ASN ALA ALA TRP TRP GLY SEQRES 17 A 830 GLY GLN PRO ILE TRP HIS THR ALA SER TYR GLN GLY LEU SEQRES 18 A 830 LYS ALA ALA THR TYR PHE TRP PRO GLY SER GLU VAL LYS SEQRES 19 A 830 ILE ASN GLY SER TYR PRO THR ILE TYR LYS VAL TYR ASN SEQRES 20 A 830 LYS SER THR PRO PHE GLU ALA ARG VAL MET GLU VAL LEU SEQRES 21 A 830 LYS TRP LEU ASP LEU PRO LYS ALA LYS ARG PRO ASP PHE SEQRES 22 A 830 SER THR LEU TYR ILE GLU GLU PRO ASP THR THR GLY HIS SEQRES 23 A 830 LYS PHE GLY PRO VAL SER GLY GLN VAL ILE LYS SER LEU SEQRES 24 A 830 GLN MET ALA ASP ARG THR LEU GLY MET LEU MET GLU GLY SEQRES 25 A 830 LEU LYS GLN ARG ASN LEU HIS ASN CYS VAL ASN LEU ILE SEQRES 26 A 830 LEU LEU ALA ASP HIS GLY MET GLU ALA ILE SER CYS ASN SEQRES 27 A 830 ARG LEU GLU TYR MET THR ASP TYR PHE ASN THR VAL ASP SEQRES 28 A 830 PHE PHE MET TYR GLU GLY ALA ALA PRO ARG ILE ARG SER SEQRES 29 A 830 LYS ASN VAL PRO LYS ASP PHE TYR THR PHE ASP SER GLU SEQRES 30 A 830 ALA ILE VAL LYS LYS LEU THR CYS ARG LYS PRO LYS GLN SEQRES 31 A 830 HIS PHE LYS ALA TYR LEU ALA LYS ASP LEU PRO LYS ARG SEQRES 32 A 830 LEU HIS PHE ALA ASN ASN ILE ARG ILE ASP LYS VAL ASN SEQRES 33 A 830 LEU MET VAL ASP ARG GLN TRP LEU ALA VAL ARG ASN LYS SEQRES 34 A 830 LYS TYR LYS TYR CYS SER GLY GLY THR HIS GLY TYR ASP SEQRES 35 A 830 ASN GLU PHE LYS SER MET GLU ALA ILE PHE LEU ALA HIS SEQRES 36 A 830 GLY PRO GLY PHE LYS GLU LYS THR GLU VAL THR SER PHE SEQRES 37 A 830 GLU ASN ILE GLU VAL TYR ASN LEU MET CYS ASP LEU LEU SEQRES 38 A 830 LYS LEU LYS PRO ALA PRO ASN ASN GLY THR HIS GLY SER SEQRES 39 A 830 LEU ASN HIS LEU LEU LYS ASN PRO PHE TYR ASN PRO SER SEQRES 40 A 830 PRO ALA LYS GLU GLN SER PRO PRO LEU TYR CYS LEU PHE SEQRES 41 A 830 GLY PRO VAL PRO SER PRO ASP VAL SER GLY CYS LYS CYS SEQRES 42 A 830 SER SER ILE THR ASP LEU GLU ALA VAL ASN GLN ARG LEU SEQRES 43 A 830 ASN LEU ILE ASP GLN ALA LYS MET GLN SER GLU ALA ASP SEQRES 44 A 830 ASN LEU PRO TYR GLY ARG PRO HIS VAL LEU GLN HIS SER SEQRES 45 A 830 LYS TYR CYS LEU LEU HIS GLN THR LYS TYR ILE SER ALA SEQRES 46 A 830 TYR SER GLN ASP ILE LEU MET PRO LEU TRP ASN SER TYR SEQRES 47 A 830 THR ILE SER LYS SER LEU VAL LYS PRO THR SER ALA PRO SEQRES 48 A 830 PRO SER ALA SER ASP CYS LEU ARG LEU ASP VAL ARG ILE SEQRES 49 A 830 PRO THR VAL GLN SER GLN THR CYS SER ASN TYR GLN PRO SEQRES 50 A 830 ASP LEU ALA ILE THR PRO GLY PHE LEU TYR PRO PRO ASP SEQRES 51 A 830 PHE SER SER SER GLY PRO GLU GLN TYR ASP ALA LEU ILE SEQRES 52 A 830 THR SER ASN ILE VAL PRO MET TYR LYS GLU PHE ALA ARG SEQRES 53 A 830 LEU TRP ASN TYR PHE HIS SER THR LEU LEU PRO LYS TYR SEQRES 54 A 830 ALA THR GLU ARG ASN GLY LEU ASN VAL ILE SER GLY PRO SEQRES 55 A 830 ILE PHE ASP TYR ASN TYR ASP GLY HIS PHE ASP PRO TYR SEQRES 56 A 830 ASP THR ILE ASP GLN TYR VAL ASN ASN THR LYS ILE PRO SEQRES 57 A 830 ILE PRO THR HIS TYR PHE VAL VAL LEU THR SER CYS GLU SEQRES 58 A 830 ASN SER THR LYS THR PRO LEU ASN CYS PRO PRO GLY SER SEQRES 59 A 830 LEU LYS VAL LEU SER PHE ILE LEU PRO HIS ARG PRO ASP SEQRES 60 A 830 ASN SER GLU SER CYS ALA ASP LYS SER PRO ASP ASN LEU SEQRES 61 A 830 TRP VAL GLU GLU ARG MET GLN THR HIS THR ALA ARG VAL SEQRES 62 A 830 ARG ASP VAL GLU LEU LEU THR GLY LEU ASP PHE TYR SER SEQRES 63 A 830 ALA LEU LYS GLN PRO LEU SER GLU THR LEU ARG LEU LYS SEQRES 64 A 830 THR PHE LEU PRO ILE PHE ILE ASN SER VAL ASN HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET NAG C 1 14 HET NAG C 2 14 HET FUC C 3 10 HET NAG D 1 14 HET FUC D 2 10 HET NAG A1001 14 HET NAG A1002 14 HET NAG A1003 14 HET ZN A1013 1 HET ZN A1014 1 HET CA A1015 1 HET AMP A1016 23 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM ZN ZINC ION HETNAM CA CALCIUM ION HETNAM AMP ADENOSINE MONOPHOSPHATE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 NAG 8(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 MAN C6 H12 O6 FORMUL 3 FUC 2(C6 H12 O5) FORMUL 8 ZN 2(ZN 2+) FORMUL 10 CA CA 2+ FORMUL 11 AMP C10 H14 N5 O7 P FORMUL 12 HOH *804(H2 O) HELIX 1 AA1 TYR A 65 LEU A 71 1 7 HELIX 2 AA2 ASN A 79 CYS A 83 5 5 HELIX 3 AA3 ASP A 108 LYS A 114 1 7 HELIX 4 AA4 ARG A 150 ASP A 158 1 9 HELIX 5 AA5 MET A 161 GLY A 171 1 11 HELIX 6 AA6 LYS A 184 GLY A 195 1 12 HELIX 7 AA7 TYR A 197 GLY A 202 1 6 HELIX 8 AA8 SER A 222 TRP A 230 5 9 HELIX 9 AA9 PRO A 234 GLN A 242 1 9 HELIX 10 AB1 LYS A 257 SER A 261 5 5 HELIX 11 AB2 PRO A 274 ASP A 287 1 14 HELIX 12 AB3 PRO A 304 GLY A 312 1 9 HELIX 13 AB4 SER A 315 ARG A 339 1 25 HELIX 14 AB5 THR A 367 TYR A 369 5 3 HELIX 15 AB6 ASP A 398 LEU A 406 1 9 HELIX 16 AB7 LYS A 421 LEU A 423 5 3 HELIX 17 AB8 PRO A 424 HIS A 428 5 5 HELIX 18 AB9 PHE A 468 GLU A 472 5 5 HELIX 19 AC1 GLU A 495 LEU A 504 1 10 HELIX 20 AC2 LEU A 518 LEU A 522 5 5 HELIX 21 AC3 ASP A 561 ARG A 568 1 8 HELIX 22 AC4 ILE A 572 LEU A 584 1 13 HELIX 23 AC5 PRO A 648 SER A 652 5 5 HELIX 24 AC6 PRO A 671 SER A 675 5 5 HELIX 25 AC7 GLY A 678 ASP A 683 1 6 HELIX 26 AC8 LYS A 695 THR A 707 1 13 HELIX 27 AC9 THR A 707 ASN A 717 1 11 HELIX 28 AD1 PRO A 737 ILE A 741 5 5 HELIX 29 AD2 PRO A 774 GLY A 776 5 3 HELIX 30 AD3 ASN A 791 CYS A 795 5 5 HELIX 31 AD4 TRP A 804 THR A 811 1 8 HELIX 32 AD5 ARG A 815 GLY A 824 1 10 HELIX 33 AD6 PRO A 834 PHE A 844 1 11 SHEET 1 AA1 8 ILE A 265 TYR A 266 0 SHEET 2 AA1 8 ALA A 246 TYR A 249 1 N ALA A 246 O ILE A 265 SHEET 3 AA1 8 PHE A 296 ILE A 301 1 O PHE A 296 N ALA A 247 SHEET 4 AA1 8 LEU A 141 MET A 146 1 N LEU A 143 O SER A 297 SHEET 5 AA1 8 ASN A 346 LEU A 350 1 O ILE A 348 N PHE A 144 SHEET 6 AA1 8 PHE A 475 HIS A 478 -1 O LEU A 476 N LEU A 349 SHEET 7 AA1 8 THR A 172 ALA A 174 -1 N THR A 172 O ALA A 477 SHEET 8 AA1 8 THR A 486 VAL A 488 1 O VAL A 488 N HIS A 173 SHEET 1 AA2 2 MET A 177 ARG A 178 0 SHEET 2 AA2 2 PHE A 491 GLU A 492 1 O PHE A 491 N ARG A 178 SHEET 1 AA3 2 MET A 208 ASP A 210 0 SHEET 2 AA3 2 GLN A 215 PHE A 217 -1 O PHE A 217 N MET A 208 SHEET 1 AA4 2 GLU A 356 ILE A 358 0 SHEET 2 AA4 2 GLY A 459 THR A 461 -1 O GLY A 459 N ILE A 358 SHEET 1 AA5 2 LEU A 363 TYR A 365 0 SHEET 2 AA5 2 LEU A 447 VAL A 449 1 O VAL A 449 N GLU A 364 SHEET 1 AA6 4 PHE A 375 TYR A 378 0 SHEET 2 AA6 4 ARG A 384 SER A 387 -1 O ARG A 386 N PHE A 376 SHEET 3 AA6 4 VAL A 438 VAL A 442 -1 O VAL A 438 N ILE A 385 SHEET 4 AA6 4 PHE A 415 LEU A 419 -1 N LYS A 416 O MET A 441 SHEET 1 AA7 2 HIS A 590 VAL A 591 0 SHEET 2 AA7 2 LEU A 825 ASP A 826 -1 O ASP A 826 N HIS A 590 SHEET 1 AA8 7 TYR A 597 HIS A 601 0 SHEET 2 AA8 7 ILE A 606 SER A 610 -1 O SER A 607 N LEU A 600 SHEET 3 AA8 7 MET A 615 ILE A 623 -1 O SER A 620 N ILE A 606 SHEET 4 AA8 7 LEU A 719 ILE A 726 -1 O VAL A 721 N TYR A 621 SHEET 5 AA8 7 HIS A 755 CYS A 763 -1 O VAL A 759 N ILE A 722 SHEET 6 AA8 7 LEU A 778 PRO A 786 -1 O LYS A 779 N SER A 762 SHEET 7 AA8 7 THR A 813 ALA A 814 -1 O ALA A 814 N SER A 782 SHEET 1 AA9 2 ILE A 664 PHE A 668 0 SHEET 2 AA9 2 ILE A 690 TYR A 694 -1 O VAL A 691 N GLY A 667 SSBOND 1 CYS A 78 CYS A 95 1555 1555 2.00 SSBOND 2 CYS A 83 CYS A 113 1555 1555 2.00 SSBOND 3 CYS A 93 CYS A 106 1555 1555 2.02 SSBOND 4 CYS A 99 CYS A 105 1555 1555 2.04 SSBOND 5 CYS A 124 CYS A 170 1555 1555 2.00 SSBOND 6 CYS A 132 CYS A 344 1555 1555 2.00 SSBOND 7 CYS A 360 CYS A 457 1555 1555 2.06 SSBOND 8 CYS A 408 CYS A 795 1555 1555 2.04 SSBOND 9 CYS A 541 CYS A 598 1555 1555 2.03 SSBOND 10 CYS A 554 CYS A 655 1555 1555 2.05 SSBOND 11 CYS A 556 CYS A 640 1555 1555 2.04 SSBOND 12 CYS A 763 CYS A 773 1555 1555 2.07 LINK ND2 ASN A 216 C1 NAG A1001 1555 1555 1.45 LINK ND2 ASN A 259 C1 NAG A1002 1555 1555 1.43 LINK ND2 ASN A 270 C1 NAG A1003 1555 1555 1.43 LINK ND2 ASN A 512 C1 NAG B 1 1555 1555 1.44 LINK ND2 ASN A 746 C1 NAG C 1 1555 1555 1.43 LINK ND2 ASN A 765 C1 NAG D 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.43 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.43 LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.46 LINK O6 NAG C 1 C1 FUC C 3 1555 1555 1.42 LINK O6 NAG D 1 C1 FUC D 2 1555 1555 1.41 LINK OD1 ASP A 147 ZN ZN A1014 1555 1555 2.01 LINK OD2 ASP A 147 ZN ZN A1014 1555 1555 2.69 LINK OG1 THR A 185 ZN ZN A1014 1555 1555 1.80 LINK OD1 ASP A 305 ZN ZN A1013 1555 1555 2.00 LINK OD2 ASP A 305 ZN ZN A1013 1555 1555 2.56 LINK NE2 HIS A 309 ZN ZN A1013 1555 1555 1.96 LINK OD2 ASP A 352 ZN ZN A1014 1555 1555 1.91 LINK NE2 HIS A 353 ZN ZN A1014 1555 1555 1.99 LINK NE2 HIS A 462 ZN ZN A1013 1555 1555 2.04 LINK OD1 ASP A 728 CA CA A1015 1555 1555 1.92 LINK OD1 ASN A 730 CA CA A1015 1555 1555 2.27 LINK OD1 ASP A 732 CA CA A1015 1555 1555 2.10 LINK O HIS A 734 CA CA A1015 1555 1555 2.25 LINK OD1 ASP A 736 CA CA A1015 1555 1555 2.07 LINK OD2 ASP A 736 CA CA A1015 1555 1555 2.48 LINK ZN ZN A1013 O1P AMP A1016 1555 1555 1.91 CISPEP 1 ALA A 89 ASN A 90 0 -10.87 CISPEP 2 CYS A 95 SER A 96 0 -26.21 CISPEP 3 GLU A 97 ASP A 98 0 13.96 CISPEP 4 TYR A 181 PRO A 182 0 -3.89 CISPEP 5 GLU A 303 PRO A 304 0 10.27 CISPEP 6 VAL A 390 PRO A 391 0 1.96 CISPEP 7 SER A 548 PRO A 549 0 -4.63 CRYST1 171.207 65.612 88.675 90.00 90.00 90.00 P 21 21 2 4 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 0.005841 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015241 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011277 0.00000