HEADER LYASE 08-AUG-22 7YQS TITLE NEUTRON STRUCTURE OF A L-RHAMNOSE-ALPHA-1,4-D-GLUCURONATE LYASE FROM TITLE 2 FUSARIUM OXYSPORUM 12S, L-RHA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-RHAMNOSE-ALPHA-1,4-D-GLUCURONATE LYASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FUSARIUM OXYSPORUM; SOURCE 3 ORGANISM_TAXID: 5507; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS NEUTRON DIFFRACTION CRYSTALLOGRAPHY, POLYSACCHARIDE LYASE, GUM KEYWDS 2 ARABIC, CARBOHYDRATE-ACTIVE ENZYME, LYASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR N.YANO,T.KONDO,K.KUSAKA,T.YAMADA,T.ARAKAWA,T.SAKAMOTO,S.FUSHINOBU REVDAT 4 27-MAR-24 7YQS 1 JRNL REVDAT 3 06-MAR-24 7YQS 1 JRNL REVDAT 2 28-FEB-24 7YQS 1 JRNL REMARK REVDAT 1 09-AUG-23 7YQS 0 JRNL AUTH N.YANO,T.KONDO,K.KUSAKA,T.ARAKAWA,T.SAKAMOTO,S.FUSHINOBU JRNL TITL CHARGE NEUTRALIZATION AND BETA-ELIMINATION CLEAVAGE JRNL TITL 2 MECHANISM OF FAMILY 42 L-RHAMNOSE-ALPHA-1,4-D-GLUCURONATE JRNL TITL 3 LYASE REVEALED USING NEUTRON CRYSTALLOGRAPHY. JRNL REF J.BIOL.CHEM. V. 300 05774 2024 JRNL REFN ESSN 1083-351X JRNL PMID 38382672 JRNL DOI 10.1016/J.JBC.2024.105774 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 115291 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5764 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 43.4200 - 3.8800 1.00 3904 205 0.1292 0.1495 REMARK 3 2 3.8800 - 3.0800 1.00 3773 199 0.1271 0.1444 REMARK 3 3 3.0800 - 2.6900 1.00 3724 196 0.1391 0.1366 REMARK 3 4 2.6900 - 2.4500 1.00 3694 194 0.1378 0.1771 REMARK 3 5 2.4500 - 2.2700 1.00 3695 195 0.1377 0.1479 REMARK 3 6 2.2700 - 2.1400 1.00 3655 193 0.1380 0.1555 REMARK 3 7 2.1400 - 2.0300 1.00 3690 193 0.1326 0.1510 REMARK 3 8 2.0300 - 1.9400 1.00 3642 193 0.1345 0.1518 REMARK 3 9 1.9400 - 1.8700 1.00 3653 192 0.1365 0.1551 REMARK 3 10 1.8700 - 1.8000 1.00 3665 192 0.1415 0.1562 REMARK 3 11 1.8000 - 1.7500 1.00 3644 192 0.1466 0.1391 REMARK 3 12 1.7500 - 1.7000 1.00 3650 193 0.1497 0.1643 REMARK 3 13 1.7000 - 1.6500 1.00 3601 189 0.1549 0.1792 REMARK 3 14 1.6500 - 1.6100 1.00 3647 192 0.1588 0.1846 REMARK 3 15 1.6100 - 1.5700 1.00 3671 194 0.1610 0.1703 REMARK 3 16 1.5700 - 1.5400 1.00 3618 189 0.1636 0.1755 REMARK 3 17 1.5400 - 1.5100 1.00 3619 191 0.1642 0.2026 REMARK 3 18 1.5100 - 1.4800 1.00 3590 189 0.1709 0.1989 REMARK 3 19 1.4800 - 1.4600 1.00 3654 192 0.1782 0.1895 REMARK 3 20 1.4600 - 1.4300 1.00 3600 190 0.1811 0.2101 REMARK 3 21 1.4300 - 1.4100 1.00 3643 191 0.1898 0.2057 REMARK 3 22 1.4100 - 1.3900 1.00 3611 191 0.1947 0.2082 REMARK 3 23 1.3900 - 1.3700 1.00 3613 190 0.2038 0.2212 REMARK 3 24 1.3700 - 1.3500 1.00 3607 190 0.2106 0.1996 REMARK 3 25 1.3500 - 1.3300 1.00 3631 191 0.2180 0.2142 REMARK 3 26 1.3300 - 1.3100 1.00 3605 190 0.2222 0.2621 REMARK 3 27 1.3100 - 1.2900 1.00 3620 190 0.2340 0.2415 REMARK 3 28 1.2900 - 1.2800 1.00 3617 190 0.2444 0.2644 REMARK 3 29 1.2800 - 1.2600 1.00 3597 189 0.2472 0.2931 REMARK 3 30 1.2600 - 1.2500 1.00 3594 189 0.2554 0.2396 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.115 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.694 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.31 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 : 0.007 7556 REMARK 3 ANGLE : 1.160 13232 REMARK 3 CHIRALITY : 0.091 529 REMARK 3 PLANARITY : 0.006 1482 REMARK 3 DIHEDRAL : 15.246 2110 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 3 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 38824 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1946 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.115 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.694 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7YQS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031333. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A 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 : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : STARGAZER REMARK 200 DATA SCALING SOFTWARE : STARGAZER REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 115388 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 43.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.88600 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: PHENIX 1.17.1_3660 REMARK 200 STARTING MODEL: 7ESK REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 12-FEB-21 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 8.50 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : SPALLATION SOURCE REMARK 230 BEAMLINE : BL-03 REMARK 230 WAVELENGTH OR RANGE (A) : 2.28-6.19 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : DIFFRACTOMETER REMARK 230 DETECTOR MANUFACTURER : IBIX REMARK 230 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 230 DATA SCALING SOFTWARE : AIMLESS REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 38826 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 230 RESOLUTION RANGE LOW (A) : 19.820 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 230 DATA REDUNDANCY : 7.900 REMARK 230 R MERGE (I) : 0.25700 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 8.4000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 230 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 230 DATA REDUNDANCY IN SHELL : 5.90 REMARK 230 R MERGE FOR SHELL (I) : 1.17400 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 1.600 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : PHENIX 1.17.1_3660 REMARK 230 STARTING MODEL: 7ESK REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION : PROTEIN 24MG/ML, REMARK 280 20MM TRIS-DCL (PD 8.0), RESERVOIR SOLUTION : 33 % (W/V) PEG 1500, REMARK 280 0.1 M TRIS-DCL (PD 8.5), 0.1 M L-RHA, PH 8.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.89000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.47500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.47500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.89000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.90000 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: 1980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLU A -1 REMARK 465 PHE A 0 REMARK 465 LEU A 420 REMARK 465 GLU A 421 REMARK 465 GLN A 422 REMARK 465 LYS A 423 REMARK 465 LEU A 424 REMARK 465 ILE A 425 REMARK 465 SER A 426 REMARK 465 GLU A 427 REMARK 465 GLU A 428 REMARK 465 ASP A 429 REMARK 465 LEU A 430 REMARK 465 ASN A 431 REMARK 465 SER A 432 REMARK 465 ALA A 433 REMARK 465 VAL A 434 REMARK 465 ASP A 435 REMARK 465 HIS A 436 REMARK 465 HIS A 437 REMARK 465 HIS A 438 REMARK 465 HIS A 439 REMARK 465 HIS A 440 REMARK 465 HIS A 441 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 SER A 141 -163.20 -102.02 REMARK 500 TYR A 150 61.05 74.73 REMARK 500 SER A 172 88.61 -169.63 REMARK 500 ASP A 238 34.74 -142.52 REMARK 500 GLU A 277 -100.82 -93.36 REMARK 500 ASP A 309 34.80 -82.10 REMARK 500 ASP A 368 43.89 -95.41 REMARK 500 ASP A 418 50.56 -90.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 604 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 28 OE2 REMARK 620 2 GLU A 154 OE1 99.5 REMARK 620 3 LEU A 206 O 82.1 72.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 605 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 171 O REMARK 620 2 ASP A 198 O 78.0 REMARK 620 3 GLU A 221 O 93.1 95.5 REMARK 620 N 1 2 DBREF 7YQS A -1 441 PDB 7YQS 7YQS -1 441 SEQRES 1 A 443 GLU PHE LEU THR VAL LYS SER THR LYS GLN TRP THR ILE SEQRES 2 A 443 GLY THR ASP VAL GLN GLY SER GLU ARG LEU ASN GLY VAL SEQRES 3 A 443 SER TYR GLN GLU ASP ALA LEU ILE THR TYR GLY ASP TYR SEQRES 4 A 443 GLN TYR VAL THR PHE TYR GLU THR ALA PRO ALA GLY TYR SEQRES 5 A 443 LEU ASN HIS PHE VAL LYS VAL GLY ARG ARG ARG VAL SER SEQRES 6 A 443 PRO SER VAL GLY ASP TRP GLU PHE LEU THR LEU ASP ASP SEQRES 7 A 443 TYR THR GLN LYS THR MET ASP GLY HIS ASN MET ILE SER SEQRES 8 A 443 MET GLY ILE SER GLY ASP GLY LYS ILE HIS LEU SER PHE SEQRES 9 A 443 ASP HIS HIS ASP VAL PRO ILE ASN TYR ARG ILE SER LYS SEQRES 10 A 443 ASN GLY ILE ALA LYS ASP VAL PRO SER LYS TRP THR SER SEQRES 11 A 443 ASP LEU PHE ASP PRO VAL VAL HIS GLU LEU VAL GLY SER SEQRES 12 A 443 GLN GLY PRO TYR SER PRO LEU THR TYR PRO ARG PHE GLU SEQRES 13 A 443 PRO LEU GLY ASN GLY ASP LEU LEU LEU GLU PHE ARG ILE SEQRES 14 A 443 GLY GLN SER GLY SER GLY ASP SER TYR ILE HIS ARG TYR SEQRES 15 A 443 SER ALA SER THR GLY LYS TRP GLN ALA TYR GLY MET TYR SEQRES 16 A 443 ILE GLN GLY ASP ASP ASN ASN ALA TYR ILE ASN GLY LEU SEQRES 17 A 443 ASP TYR LEU ASP GLY LYS LEU TYR THR SER TRP THR VAL SEQRES 18 A 443 ARG GLU THR PRO ASN ALA ASP THR ASN HIS GLY VAL TYR SEQRES 19 A 443 PHE ALA TYR SER ASN ASP ASP GLY LYS THR TRP PHE ASN SEQRES 20 A 443 THR ASN ASP THR LYS LEU THR LYS PRO ILE SER THR SER SEQRES 21 A 443 ASP ASP SER THR LEU ILE TRP ASP ILE PRO GLN ASN SER SEQRES 22 A 443 ARG MET VAL ASN GLN GLU GLY GLN LEU ILE ASP THR LYS SEQRES 23 A 443 GLY ARG PHE HIS ILE LEU MET ARG ASP LEU LEU SER GLY SEQRES 24 A 443 GLU HIS GLN TYR GLN HIS TYR LEU ARG LYS ALA ASP GLY SEQRES 25 A 443 THR TRP THR LYS ASN ALA ILE ASN PRO ALA GLY LEU ASN SEQRES 26 A 443 GLY PRO ASP LEU TYR ASP PRO ARG GLY LYS LEU ALA GLY SEQRES 27 A 443 ASP ALA SER GLY GLU TYR LEU PHE GLY ILE LEU PRO ASP SEQRES 28 A 443 PRO VAL LYS GLN SER THR GLY ILE TYR VAL ALA THR ALA SEQRES 29 A 443 SER LYS ASP PHE LYS ASP TRP LYS SER LEU ALA GLU ILE SEQRES 30 A 443 PRO ASN THR SER THR GLU PRO LEU PHE ASP LYS THR ARG SEQRES 31 A 443 LEU HIS GLU SER GLY ILE LEU SER VAL PHE VAL ARG GLN SEQRES 32 A 443 ALA GLY GLY PHE PRO ASP ARG LYS LEU GLN VAL TRP ASP SEQRES 33 A 443 PHE GLU LEU ASP LEU LEU GLU GLN LYS LEU ILE SER GLU SEQRES 34 A 443 GLU ASP LEU ASN SER ALA VAL ASP HIS HIS HIS HIS HIS SEQRES 35 A 443 HIS HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET MAN B 5 11 HET MAN B 6 11 HET MAN B 7 11 HET RAM A 601 23 HET ACT A 602 4 HET TRS A 603 18 HET CA A 604 1 HET NA A 605 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM RAM ALPHA-L-RHAMNOPYRANOSE HETNAM ACT ACETATE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM CA CALCIUM ION HETNAM NA SODIUM ION 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 RAM ALPHA-L-RHAMNOSE; 6-DEOXY-ALPHA-L-MANNOPYRANOSE; L- HETSYN 2 RAM RHAMNOSE; RHAMNOSE HETSYN TRS TRIS BUFFER FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 BMA C6 H12 O6 FORMUL 2 MAN 4(C6 H12 O6) FORMUL 3 RAM C6 H12 O5 FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 CA CA 2+ FORMUL 7 NA NA 1+ FORMUL 8 HOH *299(H2 O) HELIX 1 AA1 THR A 127 PHE A 131 5 5 HELIX 2 AA2 ASN A 224 ASP A 226 5 3 HELIX 3 AA3 ASP A 259 SER A 261 5 3 HELIX 4 AA4 SER A 363 ASP A 365 5 3 HELIX 5 AA5 ASP A 385 GLY A 393 1 9 SHEET 1 AA1 4 VAL A 3 THR A 13 0 SHEET 2 AA1 4 LYS A 409 LEU A 417 -1 O GLU A 416 N LYS A 4 SHEET 3 AA1 4 ILE A 394 ARG A 400 -1 N LEU A 395 O PHE A 415 SHEET 4 AA1 4 LEU A 383 PHE A 384 -1 N LEU A 383 O PHE A 398 SHEET 1 AA2 4 LEU A 31 TYR A 34 0 SHEET 2 AA2 4 TYR A 37 THR A 45 -1 O TYR A 39 N ILE A 32 SHEET 3 AA2 4 HIS A 53 ARG A 61 -1 O LYS A 56 N PHE A 42 SHEET 4 AA2 4 GLU A 70 GLN A 79 -1 O GLN A 79 N HIS A 53 SHEET 1 AA3 3 ILE A 88 ILE A 92 0 SHEET 2 AA3 3 ILE A 98 PHE A 102 -1 O HIS A 99 N GLY A 91 SHEET 3 AA3 3 TYR A 111 ILE A 113 -1 O ARG A 112 N LEU A 100 SHEET 1 AA4 5 LEU A 148 PRO A 155 0 SHEET 2 AA4 5 LEU A 161 GLN A 169 -1 O LEU A 162 N GLU A 154 SHEET 3 AA4 5 SER A 172 TYR A 180 -1 O TYR A 180 N LEU A 161 SHEET 4 AA4 5 TRP A 187 GLN A 195 -1 O GLN A 188 N ARG A 179 SHEET 5 AA4 5 ILE A 255 SER A 256 1 O ILE A 255 N GLN A 195 SHEET 1 AA5 4 ASN A 200 ILE A 203 0 SHEET 2 AA5 4 LYS A 212 ARG A 220 -1 O THR A 218 N TYR A 202 SHEET 3 AA5 4 ASN A 228 SER A 236 -1 O TYR A 232 N TRP A 217 SHEET 4 AA5 4 TRP A 243 PHE A 244 -1 O PHE A 244 N TYR A 235 SHEET 1 AA6 4 ASP A 207 LEU A 209 0 SHEET 2 AA6 4 LYS A 212 ARG A 220 -1 O TYR A 214 N ASP A 207 SHEET 3 AA6 4 ASN A 228 SER A 236 -1 O TYR A 232 N TRP A 217 SHEET 4 AA6 4 LEU A 263 TRP A 265 -1 O ILE A 264 N VAL A 231 SHEET 1 AA7 4 GLY A 278 ILE A 281 0 SHEET 2 AA7 4 PHE A 287 ASP A 293 -1 O HIS A 288 N LEU A 280 SHEET 3 AA7 4 GLN A 300 ARG A 306 -1 O GLN A 302 N MET A 291 SHEET 4 AA7 4 TRP A 312 ILE A 317 -1 O ASN A 315 N HIS A 303 SHEET 1 AA8 4 LYS A 333 GLY A 336 0 SHEET 2 AA8 4 TYR A 342 ASP A 349 -1 O PHE A 344 N ALA A 335 SHEET 3 AA8 4 SER A 354 THR A 361 -1 O SER A 354 N ASP A 349 SHEET 4 AA8 4 LYS A 370 PRO A 376 -1 O LEU A 372 N ILE A 357 LINK ND2 ASN A 247 C1 NAG B 1 1555 1555 1.46 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.42 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK O6 BMA B 3 C1 MAN B 4 1555 1555 1.45 LINK O3 BMA B 3 C1 MAN B 7 1555 1555 1.45 LINK O3 MAN B 4 C1 MAN B 5 1555 1555 1.44 LINK O6 MAN B 4 C1 MAN B 6 1555 1555 1.43 LINK OE2 GLU A 28 CA CA A 604 1555 1555 2.30 LINK OE1 GLU A 154 CA CA A 604 1555 1555 2.35 LINK O GLY A 171 NA NA A 605 1555 1555 2.55 LINK O ASP A 198 NA NA A 605 1555 1555 2.51 LINK O LEU A 206 CA CA A 604 1555 1555 2.39 LINK O GLU A 221 NA NA A 605 1555 1555 2.39 CISPEP 1 GLU A 28 ASP A 29 0 4.56 CISPEP 2 SER A 63 PRO A 64 0 4.34 CISPEP 3 GLY A 143 PRO A 144 0 12.92 CISPEP 4 SER A 146 PRO A 147 0 -7.91 CISPEP 5 LYS A 253 PRO A 254 0 -1.38 CISPEP 6 PHE A 405 PRO A 406 0 1.53 CRYST1 57.780 65.800 108.950 90.00 90.00 90.00 P 21 21 21 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 0.017307 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009179 0.00000