HEADER SUGAR BINDING PROTEIN 04-JAN-16 5HCH TITLE X-RAY STRUCTURE OF A LECTIN-BOUND DNA DUPLEX CONTAINING AN UNNATURAL TITLE 2 PHENANTHRENYL PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: FUCOSE-BINDING LECTIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FUCOSE-BINDING LECTIN II (PA-IIL),FUCOSE-BINDING LECTIN PA- COMPND 5 IIL,PHOTOPEXIN A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*TP*TP*(DF)P*TP*AP*TP*CP*GP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*GP*CP*GP*AP*TP*AP*(DF)P*AP*AP*TP*GP*CP*G)-3'); COMPND 13 CHAIN: E; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: LECB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, SOURCE 5 AN447_15925, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, SOURCE 6 APG04_23970, APG05_03535, APG06_28020, APG07_27985, ERS445055_01627, SOURCE 7 PA8380_17510, PAERUG_E15_LONDON_28_01_14_00983, SOURCE 8 PAERUG_P32_LONDON_17_VIM_2_10_11_00423, PAMH19_1713, PAO1OR1608; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS LECB, COMPLEX, ARTIFICIAL DNA, PHENANTHRENE, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.ROETHLISBERGER,A.ISTRATE,M.J.MARCAIDA LOPEZ,R.VISINI,A.STOCKER, AUTHOR 2 C.J.LEUMANN REVDAT 5 10-JAN-24 5HCH 1 REMARK REVDAT 4 29-JUL-20 5HCH 1 REMARK LINK SITE ATOM REVDAT 3 13-SEP-17 5HCH 1 REMARK REVDAT 2 30-MAR-16 5HCH 1 JRNL REVDAT 1 02-MAR-16 5HCH 0 JRNL AUTH P.ROETHLISBERGER,A.ISTRATE,M.J.MARCAIDA LOPEZ,R.VISINI, JRNL AUTH 2 A.STOCKER,J.L.REYMOND,C.J.LEUMANN JRNL TITL X-RAY STRUCTURE OF A LECTIN-BOUND DNA DUPLEX CONTAINING AN JRNL TITL 2 UNNATURAL PHENANTHRENYL PAIR. JRNL REF CHEM.COMMUN.(CAMB.) V. 52 4749 2016 JRNL REFN ESSN 1364-548X JRNL PMID 26898721 JRNL DOI 10.1039/C6CC00374E REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 5373 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 538 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 46.6215 - 4.6026 1.00 1335 149 0.2025 0.2234 REMARK 3 2 4.6026 - 3.6537 1.00 1218 135 0.2380 0.2790 REMARK 3 3 3.6537 - 3.1919 1.00 1187 132 0.2365 0.2536 REMARK 3 4 3.1919 - 2.9002 0.94 1095 122 0.2874 0.3669 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.00 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 1457 REMARK 3 ANGLE : 2.121 2096 REMARK 3 CHIRALITY : 0.026 248 REMARK 3 PLANARITY : 0.022 184 REMARK 3 DIHEDRAL : 23.367 533 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -30.2495 76.3711 45.5062 REMARK 3 T TENSOR REMARK 3 T11: 0.2992 T22: 0.6137 REMARK 3 T33: 0.8695 T12: -0.3256 REMARK 3 T13: -0.0147 T23: -0.1619 REMARK 3 L TENSOR REMARK 3 L11: 0.9534 L22: 2.8749 REMARK 3 L33: 2.9723 L12: -0.1726 REMARK 3 L13: 0.2247 L23: 0.0187 REMARK 3 S TENSOR REMARK 3 S11: -0.2259 S12: -0.1920 S13: 0.0235 REMARK 3 S21: 0.8077 S22: -0.0191 S23: -0.6621 REMARK 3 S31: 0.0478 S32: 0.7103 S33: 0.2871 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 5HCH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216504. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5374 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 1OXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M SODIUM ACETATE TRIHYDRATE, 0.1 REMARK 280 M TRIS HYDROCHLORIDE, 30% W/V PEG4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 136.55200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.27600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 136.55200 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.27600 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 136.55200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 68.27600 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 136.55200 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 68.27600 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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 APPLY THE FOLLOWING TO CHAINS: A, B, E REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -90.67650 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 157.05631 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 68.27600 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 -90.67650 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 157.05631 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 68.27600 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA B 101 LIES ON A SPECIAL POSITION. 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 P DG E 14 P01 61J E 101 0.08 REMARK 500 O VAL A 32 OE1 GLU A 35 1.29 REMARK 500 O VAL A 32 CD GLU A 35 1.61 REMARK 500 CB ASN A 33 OE2 GLU A 35 1.85 REMARK 500 CD1 LEU A 8 OG SER A 57 1.85 REMARK 500 O ASN A 33 OE2 GLU A 35 1.91 REMARK 500 C ASN A 33 OE2 GLU A 35 1.99 REMARK 500 O VAL A 32 OE2 GLU A 35 2.05 REMARK 500 CA ASN A 33 OE2 GLU A 35 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OXT GLY A 114 O02 61J E 101 12585 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DT B 5 O3' DT B 6 P -0.149 REMARK 500 DT E 18 O3' DA E 19 P -0.096 REMARK 500 DA E 21 O5' DA E 21 C5' 0.115 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER A 59 C - N - CA ANGL. DEV. = -27.6 DEGREES REMARK 500 SER A 59 O - C - N ANGL. DEV. = -23.9 DEGREES REMARK 500 DT B 8 C3' - O3' - P ANGL. DEV. = 8.5 DEGREES REMARK 500 DA B 9 O3' - P - OP1 ANGL. DEV. = 9.2 DEGREES REMARK 500 DA E 21 O5' - C5' - C4' ANGL. DEV. = 29.7 DEGREES REMARK 500 DA E 21 P - O5' - C5' ANGL. DEV. = 20.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 21 51.36 -141.48 REMARK 500 SER A 60 -60.27 -93.03 REMARK 500 GLU A 86 -46.32 -140.31 REMARK 500 THR A 98 -1.98 -140.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 59 -30.61 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 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 21 O REMARK 620 2 ASP A 101 OD2 171.8 REMARK 620 3 ASN A 103 OD1 98.8 78.9 REMARK 620 4 ASP A 104 OD1 83.5 104.1 86.3 REMARK 620 5 GLY A 114 O 61.9 116.0 37.2 79.2 REMARK 620 6 GLY A 114 OXT 59.5 118.3 39.5 80.0 2.5 REMARK 620 7 61J E 101 O4 132.3 53.8 122.7 77.5 150.3 152.4 REMARK 620 8 61J E 101 O02 85.9 93.6 159.8 113.7 144.4 141.9 63.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 95 OE1 REMARK 620 2 GLU A 95 OE2 54.4 REMARK 620 3 ASP A 99 OD1 81.0 115.2 REMARK 620 4 ASP A 101 OD1 78.2 115.8 93.8 REMARK 620 5 ASP A 104 OD1 127.5 98.2 145.8 77.0 REMARK 620 6 ASP A 104 OD2 95.8 52.8 164.8 100.2 45.5 REMARK 620 7 61J E 101 O5 133.8 85.5 100.0 146.7 74.6 71.4 REMARK 620 8 61J E 101 O4 149.8 154.4 74.9 85.5 71.6 112.1 69.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OXC RELATED DB: PDB REMARK 900 1OXC CONTAINS THE SAME PROTEIN COMPLEXED TO FUCOSE DBREF1 5HCH A 1 114 UNP A0A069Q9V4_PSEAI DBREF2 5HCH A A0A069Q9V4 2 115 DBREF 5HCH B 1 13 PDB 5HCH 5HCH 1 13 DBREF 5HCH E 14 26 PDB 5HCH 5HCH 14 26 SEQRES 1 A 114 ALA THR GLN GLY VAL PHE THR LEU PRO ALA ASN THR ARG SEQRES 2 A 114 PHE GLY VAL THR ALA PHE ALA ASN SER SER GLY THR GLN SEQRES 3 A 114 THR VAL ASN VAL LEU VAL ASN ASN GLU THR ALA ALA THR SEQRES 4 A 114 PHE SER GLY GLN SER THR ASN ASN ALA VAL ILE GLY THR SEQRES 5 A 114 GLN VAL LEU ASN SER GLY SER SER GLY LYS VAL GLN VAL SEQRES 6 A 114 GLN VAL SER VAL ASN GLY ARG PRO SER ASP LEU VAL SER SEQRES 7 A 114 ALA GLN VAL ILE LEU THR ASN GLU LEU ASN PHE ALA LEU SEQRES 8 A 114 VAL GLY SER GLU ASP GLY THR ASP ASN ASP TYR ASN ASP SEQRES 9 A 114 ALA VAL VAL VAL ILE ASN TRP PRO LEU GLY SEQRES 1 B 13 DC DG DC DA DT DT 61H DT DA DT DC DG DC SEQRES 1 E 13 DG DC DG DA DT DA 61H DA DA DT DG DC DG HET 61H B 7 25 HET 61H E 20 25 HET CA A 201 1 HET CA A 202 1 HET NA B 101 1 HET 61J E 101 16 HETNAM 61H (1R)-1,4-ANHYDRO-2-DEOXY-5-O-[(S)-HYDROXY(OXIDO)- HETNAM 2 61H LAMBDA~5~-PHOSPHANYL]-1-PHENANTHREN-2-YL-D-ERYTHRO- HETNAM 3 61H PENTITOL HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM 61J (6S)-2,6-ANHYDRO-1-DEOXY-6-(2-{[(S)-HYDROXY(OXIDO)- HETNAM 2 61J LAMBDA~5~-PHOSPHANYL]OXY}ETHYL)-D-GALACTITOL FORMUL 2 61H 2(C19 H19 O5 P) FORMUL 4 CA 2(CA 2+) FORMUL 6 NA NA 1+ FORMUL 7 61J C8 H17 O7 P FORMUL 8 HOH *26(H2 O) SHEET 1 AA1 4 VAL A 5 THR A 7 0 SHEET 2 AA1 4 LYS A 62 VAL A 69 -1 O VAL A 63 N PHE A 6 SHEET 3 AA1 4 ARG A 13 VAL A 32 -1 N ASN A 29 O GLN A 66 SHEET 4 AA1 4 ARG A 72 PRO A 73 0 SHEET 1 AA2 6 GLU A 35 ASN A 56 0 SHEET 2 AA2 6 ARG A 13 VAL A 32 -1 N VAL A 30 O ALA A 38 SHEET 3 AA2 6 LYS A 62 VAL A 69 -1 O GLN A 66 N ASN A 29 SHEET 4 AA2 6 ALA A 105 TRP A 111 0 SHEET 5 AA2 6 LEU A 87 GLU A 95 -1 N ALA A 90 O ILE A 109 SHEET 6 AA2 6 ASP A 75 LEU A 83 -1 N VAL A 77 O GLY A 93 LINK O3' DT B 6 P 61H B 7 1555 1555 1.61 LINK O3' 61H B 7 P DT B 8 1555 1555 1.61 LINK P DG E 14 O8 61J E 101 1555 1555 1.62 LINK P DG E 14 O06 61J E 101 1555 1555 1.48 LINK P DG E 14 O07 61J E 101 1555 1555 1.48 LINK O5' DG E 14 P01 61J E 101 1555 1555 1.60 LINK O3' DA E 19 P 61H E 20 1555 1555 1.61 LINK O3' 61H E 20 P DA E 21 1555 1555 1.61 LINK O ASN A 21 CA CA A 202 1555 1555 2.40 LINK OE1 GLU A 95 CA CA A 201 1555 1555 2.53 LINK OE2 GLU A 95 CA CA A 201 1555 1555 2.24 LINK OD1 ASP A 99 CA CA A 201 1555 1555 2.49 LINK OD1 ASP A 101 CA CA A 201 1555 1555 2.52 LINK OD2 ASP A 101 CA CA A 202 1555 1555 2.90 LINK OD1 ASN A 103 CA CA A 202 1555 1555 2.60 LINK OD1 ASP A 104 CA CA A 201 1555 1555 2.91 LINK OD2 ASP A 104 CA CA A 201 1555 1555 2.75 LINK OD1 ASP A 104 CA CA A 202 1555 1555 2.44 LINK O GLY A 114 CA CA A 202 1555 12585 2.47 LINK OXT GLY A 114 CA CA A 202 1555 12585 2.88 LINK CA CA A 201 O5 61J E 101 1555 1555 2.72 LINK CA CA A 201 O4 61J E 101 1555 1555 2.28 LINK CA CA A 202 O4 61J E 101 1555 1555 2.48 LINK CA CA A 202 O02 61J E 101 1555 1555 2.39 CISPEP 1 TRP A 111 PRO A 112 0 2.20 CRYST1 60.451 60.451 204.828 90.00 90.00 120.00 P 62 2 2 12 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 0.016542 0.009551 0.000000 0.00000 SCALE2 0.000000 0.019101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004882 0.00000