HEADER TRANSFERASE 01-MAR-15 4YIB OBSLTE 13-JUL-16 4YIB TITLE SNM-COMPLEX (LYTIC TRANSGLYCOSYLASE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSGLYCOSYLASE SLT DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 40-616; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS NM422; SOURCE 3 ORGANISM_TAXID: 1095701; SOURCE 4 GENE: NMNM422_1969; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GOLD KEYWDS PEPTIDOGLYCAN FRAGMENT RELEASE ENZYME, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.H.WILLIAMS,I.G.BONECA REVDAT 3 23-JUN-21 4YIB 1 OBSLTE COMPND REMARK HETNAM REVDAT 3 2 1 HETSYN LINK SITE ATOM REVDAT 2 13-JUL-16 4YIB 1 REVDAT 1 29-JUN-16 4YIB 0 JRNL AUTH A.H.WILLIAMS,R.WHEELER,S.HICHAM,A.HAOUZ,M.K.TAHA,I.G.BONECA JRNL TITL STRUCTURAL CHARACTERIZATION OF THE LYTIC TRANSGLYCOSYLASE JRNL TITL 2 DEPENDENT MECHANISM OF CYTOTOXIC PEPTIDOGLYCAN FRAGMENT JRNL TITL 3 RELEASE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 89285 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4700 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6099 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 321 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4490 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.070 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.124 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4679 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4419 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6347 ; 2.212 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10074 ; 1.010 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 5.571 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 229 ;38.551 ;23.057 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 722 ;12.742 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 52 ;18.169 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 683 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5428 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1142 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 4YIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 OBSOLETION UPON AUTHORS REQUEST, NO KNOWN SUPERSEDING ENTRY REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207508. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979260 REMARK 200 MONOCHROMATOR : SE FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 45.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.10630 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, 0.01M TRI SODIUM CITRATE REMARK 280 CRYSTALS APPEARED FROM 0.05-0.10 M TRI SODIUM CITRATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 33.55000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.55000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.30000 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: 2000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 21.0 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 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 1114 O HOH A 1115 2.13 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 O HOH A 979 O HOH A 1017 3656 2.05 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 GLU A 127 CD GLU A 127 OE2 -0.079 REMARK 500 ARG A 209 CZ ARG A 209 NH1 0.110 REMARK 500 ARG A 408 CZ ARG A 408 NH1 0.080 REMARK 500 GLU A 416 CD GLU A 416 OE1 -0.098 REMARK 500 GLY A 487 N GLY A 487 CA 0.100 REMARK 500 ARG A 506 CZ ARG A 506 NH1 0.138 REMARK 500 GLU A 580 CG GLU A 580 CD 0.105 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 ARG A 191 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 GLY A 204 C - N - CA ANGL. DEV. = -16.8 DEGREES REMARK 500 ARG A 209 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 209 NE - CZ - NH2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG A 222 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 MSE A 234 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 MSE A 234 CB - CG - SE ANGL. DEV. = -18.2 DEGREES REMARK 500 ARG A 243 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 265 CB - CG - OD1 ANGL. DEV. = -6.7 DEGREES REMARK 500 TYR A 284 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 290 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 290 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP A 295 CB - CG - OD1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 322 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 366 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 366 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 396 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 408 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 GLY A 413 C - N - CA ANGL. DEV. = -13.8 DEGREES REMARK 500 ASP A 415 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 451 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 GLY A 487 C - N - CA ANGL. DEV. = -14.2 DEGREES REMARK 500 ARG A 506 NE - CZ - NH1 ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 506 NE - CZ - NH2 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG A 538 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 557 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 557 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 582 NE - CZ - NH1 ANGL. DEV. = 6.3 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 GLN A 186 62.15 -105.92 REMARK 500 THR A 205 -141.40 -128.67 REMARK 500 SER A 454 53.14 -141.25 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 A1645 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A1678 DISTANCE = 6.00 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FLC A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG A REMARK 800 701 through NAG A 704 DBREF 4YIB A 40 616 UNP L5P0P1 L5P0P1_NEIME 40 616 SEQRES 1 A 577 ALA ASP LEU SER ALA SER VAL PRO THR ARG PRO ALA GLU SEQRES 2 A 577 PRO GLU ARG LYS THR LEU ALA ASP TYR GLY GLY TYR PRO SEQRES 3 A 577 SER ALA LEU ASP ALA VAL LYS GLN LYS ASN ASP ALA ALA SEQRES 4 A 577 VAL ALA ALA TYR LEU GLU ASN ALA GLY ASP SER ALA MSE SEQRES 5 A 577 ALA GLU ASN VAL ARG ASN GLU TRP LEU LYS SER LEU GLY SEQRES 6 A 577 ALA ARG ARG GLN TRP THR LEU PHE ALA GLN GLU TYR ALA SEQRES 7 A 577 LYS LEU GLU PRO ALA GLY ARG ALA GLN GLU VAL GLU CYS SEQRES 8 A 577 TYR ALA ASP SER SER ARG ASN ASP TYR THR ARG ALA ALA SEQRES 9 A 577 GLU LEU VAL LYS ASN THR GLY LYS LEU PRO SER GLY CYS SEQRES 10 A 577 THR LYS LEU LEU GLU GLN ALA ALA ALA SER GLY LEU LEU SEQRES 11 A 577 ASP GLY ASN ASP ALA TRP ARG ARG VAL ARG GLY LEU LEU SEQRES 12 A 577 ALA GLY ARG GLN THR THR ASP ALA ARG ASN LEU ALA ALA SEQRES 13 A 577 ALA LEU GLY SER PRO PHE ASP GLY GLY THR GLN GLY SER SEQRES 14 A 577 ARG GLU TYR ALA LEU LEU ASN VAL ILE GLY LYS GLU ALA SEQRES 15 A 577 ARG LYS SER PRO ASN ALA ALA ALA LEU LEU SER GLU MSE SEQRES 16 A 577 GLU SER GLY LEU SER LEU GLU GLN ARG SER PHE ALA TRP SEQRES 17 A 577 GLY VAL LEU GLY HIS TYR GLN SER GLN ASN LEU ASN VAL SEQRES 18 A 577 PRO ALA ALA LEU ASP TYR TYR GLY LYS VAL ALA ASP ARG SEQRES 19 A 577 ARG GLN LEU THR ASP ASP GLN ILE GLU TRP TYR ALA ARG SEQRES 20 A 577 ALA ALA LEU ARG ALA ARG ARG TRP ASP GLU LEU ALA SER SEQRES 21 A 577 VAL ILE SER HIS MSE PRO GLU LYS LEU GLN LYS SER PRO SEQRES 22 A 577 THR TRP LEU TYR TRP LEU ALA ARG SER ARG ALA ALA THR SEQRES 23 A 577 GLY ASN THR GLN GLU ALA GLU LYS LEU TYR LYS GLN ALA SEQRES 24 A 577 ALA ALA THR GLY ARG ASN PHE TYR ALA VAL LEU ALA GLY SEQRES 25 A 577 GLU GLU LEU GLY ARG LYS ILE ASP THR ARG ASN ASN VAL SEQRES 26 A 577 PRO ASP ALA GLY LYS ASN SER VAL ARG ARG MSE ALA GLU SEQRES 27 A 577 ASP GLY ALA VAL LYS ARG ALA LEU VAL LEU PHE GLN ASN SEQRES 28 A 577 SER GLN SER ALA GLY ASP ALA LYS MSE ARG ARG GLN ALA SEQRES 29 A 577 GLN ALA GLU TRP ARG PHE ALA THR ARG GLY PHE ASP GLU SEQRES 30 A 577 ASP LYS LEU LEU THR ALA ALA GLN THR ALA PHE ASP HIS SEQRES 31 A 577 GLY PHE TYR ASP MSE ALA VAL ASN SER ALA GLU ARG THR SEQRES 32 A 577 ASP ARG LYS LEU ASN TYR THR LEU ARG TYR ILE SER PRO SEQRES 33 A 577 PHE LYS ASP THR VAL ILE ARG HIS ALA GLN ASN VAL ASN SEQRES 34 A 577 VAL ASP PRO ALA TRP VAL TYR GLY LEU ILE ARG GLN GLU SEQRES 35 A 577 SER ARG PHE VAL ILE GLY ALA GLN SER ARG VAL GLY ALA SEQRES 36 A 577 GLN GLY LEU MSE GLN VAL MSE PRO ALA THR ALA ARG GLU SEQRES 37 A 577 ILE ALA GLY LYS ILE GLY MSE ASP ALA ALA GLN LEU TYR SEQRES 38 A 577 THR ALA ASP GLY ASN ILE ARG MSE GLY THR TRP TYR MSE SEQRES 39 A 577 ALA ASP THR LYS ARG ARG LEU GLN ASN ASN GLU VAL LEU SEQRES 40 A 577 ALA THR ALA GLY TYR ASN ALA GLY PRO GLY ARG ALA ARG SEQRES 41 A 577 ARG TRP GLN ALA ASP THR PRO LEU GLU GLY ALA VAL TYR SEQRES 42 A 577 ALA GLU THR ILE PRO PHE SER GLU THR ARG ASP TYR VAL SEQRES 43 A 577 LYS LYS VAL MSE ALA ASN ALA ALA TYR TYR ALA ALA LEU SEQRES 44 A 577 PHE GLY ALA PRO HIS ILE PRO LEU LYS GLN ARG MSE GLY SEQRES 45 A 577 ILE VAL PRO ALA ARG MODRES 4YIB MSE A 91 MET MODIFIED RESIDUE MODRES 4YIB MSE A 498 MET MODIFIED RESIDUE HET MSE A 91 8 HET MSE A 234 8 HET MSE A 304 8 HET MSE A 375 8 HET MSE A 399 8 HET MSE A 434 8 HET MSE A 498 8 HET MSE A 501 16 HET MSE A 514 8 HET MSE A 528 8 HET MSE A 533 8 HET MSE A 589 8 HET MSE A 610 8 HET NAG B 1 15 HET NAG B 2 14 HET NAG B 3 14 HET NAG B 4 14 HET FLC A 705 13 HETNAM MSE SELENOMETHIONINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FLC CITRATE ANION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 1 MSE 13(C5 H11 N O2 SE) FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 3 FLC C6 H5 O7 3- FORMUL 4 HOH *900(H2 O) HELIX 1 AA1 PRO A 53 GLN A 73 1 21 HELIX 2 AA2 ASN A 75 ASN A 85 1 11 HELIX 3 AA3 SER A 89 ARG A 106 1 18 HELIX 4 AA4 GLN A 108 ALA A 117 1 10 HELIX 5 AA5 LYS A 118 LEU A 119 5 2 HELIX 6 AA6 GLU A 120 ARG A 124 5 5 HELIX 7 AA7 ALA A 125 ARG A 136 1 12 HELIX 8 AA8 ARG A 141 VAL A 146 1 6 HELIX 9 AA9 PRO A 153 SER A 166 1 14 HELIX 10 AB1 ASP A 170 GLY A 184 1 15 HELIX 11 AB2 GLN A 186 LEU A 197 1 12 HELIX 12 AB3 THR A 205 LEU A 213 1 9 HELIX 13 AB4 LEU A 213 GLY A 218 1 6 HELIX 14 AB5 GLU A 220 SER A 224 5 5 HELIX 15 AB6 ASN A 226 GLU A 235 1 10 HELIX 16 AB7 SER A 236 LEU A 238 5 3 HELIX 17 AB8 SER A 239 ASN A 257 1 19 HELIX 18 AB9 ASN A 259 LYS A 269 1 11 HELIX 19 AC1 ASP A 272 LEU A 276 5 5 HELIX 20 AC2 THR A 277 ARG A 292 1 16 HELIX 21 AC3 ARG A 293 HIS A 303 1 11 HELIX 22 AC4 PRO A 305 LYS A 310 1 6 HELIX 23 AC5 SER A 311 THR A 325 1 15 HELIX 24 AC6 ASN A 327 ALA A 340 1 14 HELIX 25 AC7 ASN A 344 LEU A 354 1 11 HELIX 26 AC8 GLY A 368 ASP A 378 1 11 HELIX 27 AC9 ASP A 378 GLY A 395 1 18 HELIX 28 AD1 ASP A 396 ARG A 412 1 17 HELIX 29 AD2 ASP A 415 HIS A 429 1 15 HELIX 30 AD3 PHE A 431 ARG A 441 1 11 HELIX 31 AD4 ASN A 447 TYR A 452 1 6 HELIX 32 AD5 PHE A 456 VAL A 467 1 12 HELIX 33 AD6 ASP A 470 ARG A 483 1 14 HELIX 34 AD7 MSE A 501 ILE A 512 1 12 HELIX 35 AD8 ASP A 515 TYR A 520 5 6 HELIX 36 AD9 THR A 521 ARG A 539 1 19 HELIX 37 AE1 ASN A 543 GLY A 554 1 12 HELIX 38 AE2 GLY A 554 TRP A 561 1 8 HELIX 39 AE3 GLY A 569 THR A 575 1 7 HELIX 40 AE4 PHE A 578 GLY A 600 1 23 HELIX 41 AE5 PRO A 605 GLY A 611 1 7 SHEET 1 AA1 2 LEU A 567 GLU A 568 0 SHEET 2 AA1 2 ILE A 612 VAL A 613 -1 O VAL A 613 N LEU A 567 SSBOND 1 CYS A 130 CYS A 156 1555 1555 2.42 LINK C ALA A 90 N MSE A 91 1555 1555 1.34 LINK C MSE A 91 N ALA A 92 1555 1555 1.32 LINK C GLU A 233 N MSE A 234 1555 1555 1.33 LINK C MSE A 234 N GLU A 235 1555 1555 1.33 LINK C HIS A 303 N MSE A 304 1555 1555 1.34 LINK C MSE A 304 N PRO A 305 1555 1555 1.34 LINK C ARG A 374 N MSE A 375 1555 1555 1.32 LINK C MSE A 375 N ALA A 376 1555 1555 1.32 LINK C LYS A 398 N MSE A 399 1555 1555 1.33 LINK C MSE A 399 N ARG A 400 1555 1555 1.31 LINK C ASP A 433 N MSE A 434 1555 1555 1.32 LINK C MSE A 434 N ALA A 435 1555 1555 1.36 LINK C LEU A 497 N MSE A 498 1555 1555 1.32 LINK C MSE A 498 N GLN A 499 1555 1555 1.36 LINK C VAL A 500 N AMSE A 501 1555 1555 1.32 LINK C VAL A 500 N BMSE A 501 1555 1555 1.33 LINK C AMSE A 501 N PRO A 502 1555 1555 1.35 LINK C BMSE A 501 N PRO A 502 1555 1555 1.36 LINK C GLY A 513 N MSE A 514 1555 1555 1.32 LINK C MSE A 514 N ASP A 515 1555 1555 1.33 LINK C ARG A 527 N MSE A 528 1555 1555 1.34 LINK C MSE A 528 N GLY A 529 1555 1555 1.33 LINK C TYR A 532 N MSE A 533 1555 1555 1.36 LINK C MSE A 533 N ALA A 534 1555 1555 1.34 LINK C VAL A 588 N MSE A 589 1555 1555 1.31 LINK C MSE A 589 N ALA A 590 1555 1555 1.30 LINK C ARG A 609 N MSE A 610 1555 1555 1.36 LINK C MSE A 610 N GLY A 611 1555 1555 1.31 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.42 LINK O4 NAG B 2 C1 NAG B 3 1555 1555 1.37 LINK O4 NAG B 3 C1 NAG B 4 1555 1555 1.47 SITE 1 AC1 15 LEU A 258 VAL A 260 PRO A 261 ARG A 290 SITE 2 AC1 15 ALA A 563 ASP A 564 HOH A 859 HOH A1141 SITE 3 AC1 15 HOH A1170 HOH A1183 HOH A1195 HOH A1244 SITE 4 AC1 15 HOH A1396 HOH A1408 HOH A1430 SITE 1 AC2 23 ASN A 215 GLU A 481 VAL A 492 GLN A 499 SITE 2 AC2 23 VAL A 500 MSE A 501 THR A 504 GLU A 507 SITE 3 AC2 23 TYR A 532 TYR A 551 ASN A 552 ALA A 553 SITE 4 AC2 23 GLY A 554 GLY A 556 ARG A 557 GLU A 580 SITE 5 AC2 23 HOH A 902 HOH A1346 HOH A1364 HOH A1615 SITE 6 AC2 23 HOH A1661 HOH A1695 HOH A1697 CRYST1 67.100 72.600 125.000 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 0.014903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013774 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008000 0.00000