HEADER SUGAR BINDING PROTEIN 21-MAR-19 6R43 TITLE STRUCTURE OF P110 FROM MYCOPLASMA GENITALIUM COMPLEXED WITH 6'-SL COMPND MOL_ID: 1; COMPND 2 MOLECULE: MGP-OPERON PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MGP3,ORF-3 PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA GENITALIUM G37; SOURCE 3 ORGANISM_TAXID: 243273; SOURCE 4 GENE: MG192; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ADHESIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.APARICIO,I.FITA REVDAT 3 24-JAN-24 6R43 1 HETSYN LINK REVDAT 2 29-JUL-20 6R43 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE ATOM REVDAT 1 10-APR-19 6R43 0 SPRSDE 10-APR-19 6R43 5MZD JRNL AUTH D.APARICIO,S.TORRES-PUIG,M.RATERA,E.QUEROL,J.PINOL,O.Q.PICH, JRNL AUTH 2 I.FITA JRNL TITL MYCOPLASMA GENITALIUM ADHESIN P110 BINDS SIALIC-ACID HUMAN JRNL TITL 2 RECEPTORS. JRNL REF NAT COMMUN V. 9 4471 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30367053 JRNL DOI 10.1038/S41467-018-06963-Y REMARK 2 REMARK 2 RESOLUTION. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 46747 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2474 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.52 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3413 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.3840 REMARK 3 BIN FREE R VALUE SET COUNT : 177 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6825 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 93.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : -0.88000 REMARK 3 B33 (A**2) : 1.25000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.298 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.319 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7037 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6200 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9580 ; 1.901 ; 1.650 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14522 ; 1.315 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 888 ; 9.183 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 334 ;38.549 ;25.060 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1136 ;20.313 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.240 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 974 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7904 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1367 ; 0.002 ; 0.020 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): 3561 ; 2.886 ; 4.721 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3560 ; 2.885 ; 4.720 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4446 ; 4.514 ; 7.082 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4447 ; 4.514 ; 7.083 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3475 ; 2.950 ; 4.828 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3471 ; 2.898 ; 4.824 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5129 ; 4.443 ; 7.153 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7565 ; 6.639 ;54.604 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7548 ; 6.630 ;54.528 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 : 1 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 25 A 1001 REMARK 3 ORIGIN FOR THE GROUP (A): 9.1887 184.3644 50.2184 REMARK 3 T TENSOR REMARK 3 T11: 0.0961 T22: 0.6258 REMARK 3 T33: 0.4333 T12: -0.1522 REMARK 3 T13: -0.0991 T23: 0.4993 REMARK 3 L TENSOR REMARK 3 L11: 1.1601 L22: 3.2688 REMARK 3 L33: 2.8830 L12: -0.7198 REMARK 3 L13: 0.5025 L23: -2.5111 REMARK 3 S TENSOR REMARK 3 S11: -0.1581 S12: 0.7347 S13: 0.6531 REMARK 3 S21: -0.2253 S22: -0.1261 S23: -0.4337 REMARK 3 S31: 0.0065 S32: 0.0121 S33: 0.2842 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6R43 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101409. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97895 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50406 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 57.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 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: PHENIX REMARK 200 STARTING MODEL: 6R3T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3350, 0.2M TRI-POTASSIUM REMARK 280 CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 1.000000 0.000000 0.000000 54.84500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 76.34500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 88.11500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 54.84500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 76.34500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 88.11500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 54.84500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 76.34500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 88.11500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 54.84500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 76.34500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 88.11500 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: 1390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 ALA A 23 REMARK 465 LEU A 24 REMARK 465 GLY A 258 REMARK 465 GLY A 259 REMARK 465 SER A 260 REMARK 465 SER A 413 REMARK 465 SER A 414 REMARK 465 SER A 415 REMARK 465 SER A 416 REMARK 465 GLY A 471 REMARK 465 ASN A 472 REMARK 465 HIS A 473 REMARK 465 THR A 474 REMARK 465 ASN A 475 REMARK 465 ASN A 476 REMARK 465 GLY A 477 REMARK 465 ASP A 592 REMARK 465 GLY A 593 REMARK 465 PHE A 594 REMARK 465 LYS A 595 REMARK 465 ARG A 596 REMARK 465 PRO A 597 REMARK 465 GLU A 598 REMARK 465 ASN A 599 REMARK 465 ARG A 600 REMARK 465 GLY A 601 REMARK 465 ALA A 602 REMARK 465 PRO A 937 REMARK 465 ALA A 938 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 OD1 ASN A 289 OG1 THR A 292 2.07 REMARK 500 O GLN A 231 OH TYR A 268 2.10 REMARK 500 N GLN A 749 OG1 THR A 753 2.15 REMARK 500 OG SER A 138 OD1 ASP A 565 2.17 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 TYR A 584 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP A 723 CB - CA - C ANGL. DEV. = -12.1 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 ASP A 33 -164.44 -160.55 REMARK 500 THR A 74 -1.05 68.87 REMARK 500 SER A 94 19.46 -162.15 REMARK 500 ASN A 95 59.74 -103.91 REMARK 500 SER A 103 -116.74 68.96 REMARK 500 GLN A 104 74.91 -159.87 REMARK 500 ASN A 136 151.31 -40.67 REMARK 500 LYS A 156 -46.44 -24.48 REMARK 500 ALA A 164 128.75 -22.04 REMARK 500 HIS A 175 -70.42 -96.80 REMARK 500 SER A 237 -69.04 -19.08 REMARK 500 THR A 243 -82.30 -109.14 REMARK 500 SER A 256 87.04 -168.84 REMARK 500 SER A 262 127.48 56.90 REMARK 500 ASP A 284 -117.83 58.87 REMARK 500 THR A 299 64.86 -101.26 REMARK 500 GLN A 330 157.13 -45.97 REMARK 500 ASN A 369 -1.94 68.80 REMARK 500 ASN A 392 -127.09 56.07 REMARK 500 SER A 410 157.58 -49.31 REMARK 500 SER A 418 118.23 -29.38 REMARK 500 ASP A 422 18.44 57.25 REMARK 500 THR A 437 -154.30 -73.70 REMARK 500 ILE A 453 -15.46 -157.00 REMARK 500 GLN A 460 -72.25 49.58 REMARK 500 ASP A 461 38.94 -175.53 REMARK 500 SER A 529 38.03 -68.67 REMARK 500 ASN A 530 -30.37 -156.29 REMARK 500 GLN A 540 38.14 75.93 REMARK 500 SER A 561 117.47 -19.64 REMARK 500 ASP A 590 173.97 166.77 REMARK 500 GLU A 700 151.06 177.32 REMARK 500 ASP A 723 166.38 -23.33 REMARK 500 PRO A 728 135.39 -36.32 REMARK 500 ASP A 731 41.82 -98.51 REMARK 500 PHE A 735 174.51 178.03 REMARK 500 ASN A 748 40.49 91.82 REMARK 500 SER A 771 138.89 -170.63 REMARK 500 SER A 794 -82.70 -88.63 REMARK 500 ASP A 795 -18.39 -144.00 REMARK 500 ASP A 836 -155.24 -109.98 REMARK 500 ASN A 864 49.19 -107.23 REMARK 500 THR A 865 70.65 -162.35 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 PRO A 135 ASN A 136 147.60 REMARK 500 SER A 178 GLY A 179 -142.26 REMARK 500 GLY A 179 GLN A 180 -147.16 REMARK 500 THR A 243 GLU A 244 -147.72 REMARK 500 HIS A 722 ASP A 723 148.80 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 K A1001 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 831 O REMARK 620 2 ARG A 834 O 76.6 REMARK 620 3 ASP A 836 OD1 117.1 95.3 REMARK 620 4 ASP A 836 OD2 74.6 88.5 42.6 REMARK 620 5 GLY A 839 O 145.7 69.4 71.6 108.2 REMARK 620 6 HOH A1138 O 136.4 121.4 101.3 138.0 64.0 REMARK 620 7 HOH A1162 O 74.6 93.9 166.6 147.6 102.8 65.5 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6R3T RELATED DB: PDB REMARK 900 6R3T CONTAINS THE SAME PROTEIN WITHOUT 6'-SIALYLLACTOSE REMARK 900 RELATED ID: 6R41 RELATED DB: PDB REMARK 900 6R41 CONTAINS THE SAME PROTEIN BUT COMPLEXED WITH 3'-SIALYLLACTOSE REMARK 900 INSTEAD OF 6'-SIALYLLACTOSE DBREF 6R43 A 23 938 UNP P22747 MGP3_MYCGE 23 938 SEQRES 1 A 916 ALA LEU ALA ASN THR PHE LEU VAL LYS GLU ASP SER LYS SEQRES 2 A 916 ASN VAL THR ALA TYR THR PRO PHE ALA THR PRO ILE THR SEQRES 3 A 916 ASP SER LYS SER ASP LEU VAL SER LEU ALA GLN LEU ASP SEQRES 4 A 916 SER SER TYR GLN ILE ALA ASP GLN THR ILE HIS ASN THR SEQRES 5 A 916 ASN LEU PHE VAL LEU PHE LYS SER ARG ASP VAL LYS VAL SEQRES 6 A 916 LYS TYR GLU SER SER GLY SER ASN ASN ILE SER PHE ASP SEQRES 7 A 916 SER THR SER GLN GLY GLU LYS PRO SER TYR VAL VAL GLU SEQRES 8 A 916 PHE THR ASN SER THR ASN ILE GLY ILE LYS TRP THR MET SEQRES 9 A 916 VAL LYS LYS TYR GLN LEU ASP VAL PRO ASN VAL SER SER SEQRES 10 A 916 ASP MET ASN GLN VAL LEU LYS ASN LEU ILE LEU GLU GLN SEQRES 11 A 916 PRO LEU THR LYS TYR THR LEU ASN SER SER LEU ALA LYS SEQRES 12 A 916 GLU LYS GLY LYS THR GLN ARG GLU VAL HIS LEU GLY SER SEQRES 13 A 916 GLY GLN ALA ASN GLN TRP THR SER GLN ARG ASN GLN HIS SEQRES 14 A 916 ASP LEU ASN ASN ASN PRO SER PRO ASN ALA SER THR GLY SEQRES 15 A 916 PHE LYS LEU THR THR GLY ASN ALA TYR ARG LYS LEU SER SEQRES 16 A 916 GLU SER TRP PRO ILE TYR GLU PRO ILE ASP GLY THR LYS SEQRES 17 A 916 GLN GLY LYS GLY LYS ASP SER SER GLY TRP SER SER THR SEQRES 18 A 916 GLU GLU ASN GLU ALA LYS ASN ASP ALA PRO SER VAL SER SEQRES 19 A 916 GLY GLY GLY SER SER SER GLY THR PHE ASN LYS TYR LEU SEQRES 20 A 916 ASN THR LYS GLN ALA LEU GLU SER ILE GLY ILE LEU PHE SEQRES 21 A 916 ASP ASP GLN THR PRO ARG ASN VAL ILE THR GLN LEU TYR SEQRES 22 A 916 TYR ALA SER THR SER LYS LEU ALA VAL THR ASN ASN HIS SEQRES 23 A 916 ILE VAL VAL MET GLY ASN SER PHE LEU PRO SER MET TRP SEQRES 24 A 916 TYR TRP VAL VAL GLU ARG SER ALA GLN GLU ASN ALA SER SEQRES 25 A 916 ASN LYS PRO THR TRP PHE ALA ASN THR ASN LEU ASP TRP SEQRES 26 A 916 GLY GLU ASP LYS GLN LYS GLN PHE VAL GLU ASN GLN LEU SEQRES 27 A 916 GLY TYR LYS GLU THR THR SER THR ASN SER HIS ASN PHE SEQRES 28 A 916 HIS SER LYS SER PHE THR GLN PRO ALA TYR LEU ILE SER SEQRES 29 A 916 GLY ILE ASP SER VAL ASN ASP GLN ILE ILE PHE SER GLY SEQRES 30 A 916 PHE LYS ALA GLY SER VAL GLY TYR ASP SER SER SER SER SEQRES 31 A 916 SER SER SER SER SER SER SER THR LYS ASP GLN ALA LEU SEQRES 32 A 916 ALA TRP SER THR THR THR SER LEU ASP SER LYS THR GLY SEQRES 33 A 916 TYR LYS ASP LEU VAL THR ASN ASP THR GLY LEU ASN GLY SEQRES 34 A 916 PRO ILE ASN GLY SER PHE SER ILE GLN ASP THR PHE SER SEQRES 35 A 916 PHE VAL VAL PRO TYR SER GLY ASN HIS THR ASN ASN GLY SEQRES 36 A 916 THR THR GLY PRO ILE LYS THR ALA TYR PRO VAL LYS LYS SEQRES 37 A 916 ASP GLN LYS SER THR VAL LYS ILE ASN SER LEU ILE ASN SEQRES 38 A 916 ALA THR PRO LEU ASN SER TYR GLY ASP GLU GLY ILE GLY SEQRES 39 A 916 VAL PHE ASP ALA LEU GLY LEU ASN TYR ASN PHE LYS SER SEQRES 40 A 916 ASN GLN GLU ARG LEU PRO SER ARG THR ASP GLN ILE PHE SEQRES 41 A 916 VAL TYR GLY ILE VAL SER PRO ASN GLU LEU ARG SER ALA SEQRES 42 A 916 LYS SER SER ALA ASP SER THR GLY SER ASP THR LYS VAL SEQRES 43 A 916 ASN TRP SER ASN THR GLN SER ARG TYR LEU PRO VAL PRO SEQRES 44 A 916 TYR ASN TYR SER GLU GLY ILE ILE ASP ALA ASP GLY PHE SEQRES 45 A 916 LYS ARG PRO GLU ASN ARG GLY ALA SER VAL THR THR PHE SEQRES 46 A 916 SER GLY LEU LYS SER ILE ALA PRO ASP GLY PHE ALA ASN SEQRES 47 A 916 SER ILE ALA ASN PHE SER VAL GLY LEU LYS ALA GLY ILE SEQRES 48 A 916 ASP PRO ASN PRO VAL MET SER GLY LYS LYS ALA ASN TYR SEQRES 49 A 916 GLY ALA VAL VAL LEU THR ARG GLY GLY VAL VAL ARG LEU SEQRES 50 A 916 ASN PHE ASN PRO GLY ASN ASP SER LEU LEU SER THR THR SEQRES 51 A 916 ASP ASN ASN ILE ALA PRO ILE SER PHE SER PHE THR PRO SEQRES 52 A 916 PHE THR ALA ALA GLU SER ALA VAL ASP LEU THR THR PHE SEQRES 53 A 916 LYS GLU VAL THR TYR ASN GLN GLU SER GLY LEU TRP SER SEQRES 54 A 916 TYR ILE PHE ASP SER SER LEU LYS PRO SER HIS ASP GLY SEQRES 55 A 916 LYS GLN THR PRO VAL THR ASP ASN MET GLY PHE SER VAL SEQRES 56 A 916 ILE THR VAL SER ARG THR GLY ILE GLU LEU ASN GLN ASP SEQRES 57 A 916 GLN ALA THR THR THR LEU ASP VAL ALA PRO SER ALA LEU SEQRES 58 A 916 ALA VAL GLN SER GLY ILE GLN SER THR THR GLN THR LEU SEQRES 59 A 916 THR GLY VAL LEU PRO LEU SER GLU GLU PHE SER ALA VAL SEQRES 60 A 916 ILE ALA LYS ASP SER ASP GLN ASN LYS ILE ASP ILE TYR SEQRES 61 A 916 LYS ASN ASN ASN GLY LEU PHE GLU ILE ASP THR GLN LEU SEQRES 62 A 916 SER ASN SER VAL ALA THR ASN ASN GLY GLY LEU ALA PRO SEQRES 63 A 916 SER TYR THR GLU ASN ARG VAL ASP ALA TRP GLY LYS VAL SEQRES 64 A 916 GLU PHE ALA ASP ASN SER VAL LEU GLN ALA ARG ASN LEU SEQRES 65 A 916 VAL ASP LYS THR VAL ASP GLU ILE ILE ASN THR PRO GLU SEQRES 66 A 916 ILE LEU ASN SER PHE PHE ARG PHE THR PRO ALA PHE GLU SEQRES 67 A 916 ASP GLN LYS ALA THR LEU VAL ALA THR LYS GLN SER ASP SEQRES 68 A 916 THR SER LEU SER VAL SER PRO ARG ILE GLN PHE LEU ASP SEQRES 69 A 916 GLY ASN PHE TYR ASP LEU ASN SER THR ILE ALA GLY VAL SEQRES 70 A 916 PRO LEU ASN ILE GLY PHE PRO SER ARG VAL PHE ALA GLY SEQRES 71 A 916 PHE ALA ALA LEU PRO ALA HET BGC B 1 12 HET GAL B 2 11 HET SIA B 3 20 HET K A1001 1 HET PO4 A1002 5 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETNAM K POTASSIUM ION HETNAM PO4 PHOSPHATE ION HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 2 SIA C11 H19 N O9 FORMUL 3 K K 1+ FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *99(H2 O) HELIX 1 AA1 LEU A 54 ALA A 58 1 5 HELIX 2 AA2 SER A 138 ASN A 147 1 10 HELIX 3 AA3 LEU A 159 ALA A 164 1 6 HELIX 4 AA4 THR A 170 LEU A 176 1 7 HELIX 5 AA5 GLN A 183 ARG A 188 1 6 HELIX 6 AA6 ASN A 189 ASP A 192 5 4 HELIX 7 AA7 ASP A 227 GLY A 232 1 6 HELIX 8 AA8 ASP A 236 THR A 243 1 8 HELIX 9 AA9 THR A 243 ALA A 252 1 10 HELIX 10 AB1 THR A 271 ILE A 278 1 8 HELIX 11 AB2 ASN A 289 THR A 299 1 11 HELIX 12 AB3 GLU A 349 GLY A 361 1 13 HELIX 13 AB4 GLY A 438 THR A 444 1 7 HELIX 14 AB5 GLU A 513 GLY A 522 1 10 HELIX 15 AB6 SER A 548 SER A 561 1 14 HELIX 16 AB7 PRO A 581 ASN A 583 5 3 HELIX 17 AB8 THR A 687 ALA A 692 1 6 HELIX 18 AB9 ASP A 694 THR A 696 5 3 HELIX 19 AC1 SER A 717 LYS A 719 5 3 HELIX 20 AC2 ASP A 750 THR A 755 5 6 HELIX 21 AC3 ASP A 812 THR A 821 1 10 HELIX 22 AC4 SER A 847 ASN A 853 1 7 HELIX 23 AC5 THR A 858 ASN A 864 1 7 HELIX 24 AC6 THR A 865 ASN A 870 1 6 SHEET 1 AA1 3 PHE A 28 LYS A 31 0 SHEET 2 AA1 3 ASN A 36 TYR A 40 -1 O TYR A 40 N PHE A 28 SHEET 3 AA1 3 SER A 52 ASP A 53 -1 O SER A 52 N VAL A 37 SHEET 1 AA2 4 TYR A 64 HIS A 72 0 SHEET 2 AA2 4 ASN A 75 SER A 82 -1 O PHE A 77 N THR A 70 SHEET 3 AA2 4 SER A 109 ASN A 116 -1 O PHE A 114 N LEU A 76 SHEET 4 AA2 4 TRP A 124 LEU A 132 -1 O LYS A 128 N GLU A 113 SHEET 1 AA3 2 VAL A 87 TYR A 89 0 SHEET 2 AA3 2 ILE A 97 PHE A 99 -1 O SER A 98 N LYS A 88 SHEET 1 AA4 6 GLY A 204 LYS A 206 0 SHEET 2 AA4 6 GLN A 423 LEU A 425 -1 O ALA A 424 N PHE A 205 SHEET 3 AA4 6 SER A 404 ASP A 408 -1 N GLY A 406 O LEU A 425 SHEET 4 AA4 6 ILE A 498 ILE A 502 -1 O ASN A 499 N TYR A 407 SHEET 5 AA4 6 ILE A 149 GLU A 151 1 N GLU A 151 O ILE A 502 SHEET 6 AA4 6 TYR A 213 ARG A 214 -1 O ARG A 214 N LEU A 150 SHEET 1 AA5 2 TYR A 223 PRO A 225 0 SHEET 2 AA5 2 TYR A 268 ASN A 270 -1 O LEU A 269 N GLU A 224 SHEET 1 AA6 2 PHE A 282 ASP A 283 0 SHEET 2 AA6 2 THR A 286 PRO A 287 -1 O THR A 286 N ASP A 283 SHEET 1 AA7 4 LYS A 301 VAL A 304 0 SHEET 2 AA7 4 HIS A 308 MET A 312 -1 O MET A 312 N LYS A 301 SHEET 3 AA7 4 TRP A 321 GLU A 326 -1 O VAL A 325 N ILE A 309 SHEET 4 AA7 4 PRO A 337 TRP A 339 -1 O THR A 338 N TYR A 322 SHEET 1 AA8 2 THR A 343 LEU A 345 0 SHEET 2 AA8 2 VAL A 568 TRP A 570 1 O TRP A 570 N ASN A 344 SHEET 1 AA9 4 TYR A 383 VAL A 391 0 SHEET 2 AA9 4 GLN A 394 LYS A 401 -1 O PHE A 400 N LEU A 384 SHEET 3 AA9 4 ILE A 541 VAL A 547 -1 O VAL A 547 N ILE A 395 SHEET 4 AA9 4 THR A 573 TYR A 577 -1 O ARG A 576 N PHE A 542 SHEET 1 AB1 2 PHE A 457 ILE A 459 0 SHEET 2 AB1 2 THR A 462 SER A 464 -1 O THR A 462 N ILE A 459 SHEET 1 AB2 2 SER A 585 GLU A 586 0 SHEET 2 AB2 2 LYS A 611 SER A 612 -1 O LYS A 611 N GLU A 586 SHEET 1 AB3 4 SER A 626 ILE A 633 0 SHEET 2 AB3 4 TYR A 646 THR A 652 -1 O GLY A 647 N GLY A 632 SHEET 3 AB3 4 GLY A 655 ASN A 662 -1 O VAL A 657 N VAL A 650 SHEET 4 AB3 4 SER A 667 LEU A 668 -1 O SER A 667 N ASN A 662 SHEET 1 AB4 4 SER A 626 ILE A 633 0 SHEET 2 AB4 4 TYR A 646 THR A 652 -1 O GLY A 647 N GLY A 632 SHEET 3 AB4 4 GLY A 655 ASN A 662 -1 O VAL A 657 N VAL A 650 SHEET 4 AB4 4 PHE A 681 PRO A 685 -1 O THR A 684 N VAL A 656 SHEET 1 AB5 4 PHE A 698 ASN A 704 0 SHEET 2 AB5 4 LEU A 709 ASP A 715 -1 O ILE A 713 N LYS A 699 SHEET 3 AB5 4 PHE A 735 THR A 743 -1 O ILE A 738 N TYR A 712 SHEET 4 AB5 4 SER A 761 SER A 771 -1 O SER A 761 N THR A 743 SHEET 1 AB6 4 THR A 775 SER A 783 0 SHEET 2 AB6 4 PHE A 786 LYS A 792 -1 O ILE A 790 N GLY A 778 SHEET 3 AB6 4 ASN A 797 ASN A 805 -1 O LYS A 798 N ALA A 791 SHEET 4 AB6 4 LEU A 808 ILE A 811 -1 O GLU A 810 N LYS A 803 SHEET 1 AB7 2 LYS A 840 PHE A 843 0 SHEET 2 AB7 2 PHE A 873 THR A 876 -1 O ARG A 874 N GLU A 842 SHEET 1 AB8 3 ALA A 884 SER A 892 0 SHEET 2 AB8 3 SER A 895 GLN A 903 -1 O ARG A 901 N THR A 885 SHEET 3 AB8 3 PHE A 909 TYR A 910 -1 O TYR A 910 N ILE A 902 SHEET 1 AB9 3 ALA A 884 SER A 892 0 SHEET 2 AB9 3 SER A 895 GLN A 903 -1 O ARG A 901 N THR A 885 SHEET 3 AB9 3 ARG A 928 ALA A 931 -1 O PHE A 930 N LEU A 896 SHEET 1 AC1 2 THR A 915 ILE A 916 0 SHEET 2 AC1 2 VAL A 919 PRO A 920 -1 O VAL A 919 N ILE A 916 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.42 LINK O6 GAL B 2 C2 SIA B 3 1555 1555 1.44 LINK O THR A 831 K K A1001 1555 1555 2.83 LINK O ARG A 834 K K A1001 1555 1555 2.76 LINK OD1 ASP A 836 K K A1001 1555 1555 2.92 LINK OD2 ASP A 836 K K A1001 1555 1555 2.94 LINK O GLY A 839 K K A1001 1555 1555 2.91 LINK K K A1001 O HOH A1138 1555 1555 2.83 LINK K K A1001 O HOH A1162 1555 1555 3.02 CRYST1 109.690 152.690 176.230 90.00 90.00 90.00 I 2 2 2 8 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 0.009117 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006549 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005674 0.00000