HEADER TRANSFERASE 02-MAR-15 4YIM OBSLTE 13-JUL-16 4YIM 6FPN TITLE STRUCTURAL CHARACTERIZATION OF THE LYTIC TRANSGLYCOSYLASE DEPENDENT TITLE 2 MECHANISM OF CYTOTOXIC PEPTIDOGLYCAN FRAGMENT RELEASE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SOLUBLE LYTIC MUREIN TRANSGLYCOSYLASE; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP B (STRAIN SOURCE 3 MC58); SOURCE 4 ORGANISM_TAXID: 122586; SOURCE 5 STRAIN: MC58; SOURCE 6 GENE: NMB1949; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: GOLD KEYWDS COMPLEX, LYTIC TRANSGLYCOSYLASE, LTGA, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.H.WILLIAMS,R.WHEELER,S.HISCHAM,A.HAOUZ,M.K.TAHA,I.G.BONECA REVDAT 4 08-NOV-23 4YIM 1 OBSLTE REVDAT 3 23-JUN-21 4YIM 1 OBSLTE REVDAT 2 13-JUL-16 4YIM 1 REVDAT 1 29-JUN-16 4YIM 0 JRNL AUTH A.H.WILLIAMS,R.WHEELER,S.HISCHAM,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. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 106106 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) : 0.188 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 11813 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7311 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.4060 REMARK 3 BIN FREE R VALUE SET COUNT : 834 REMARK 3 BIN FREE R VALUE : 0.4390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 912 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.22000 REMARK 3 B22 (A**2) : -0.09000 REMARK 3 B33 (A**2) : -0.13000 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): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.146 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4681 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6347 ; 2.160 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 589 ; 5.225 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 229 ;37.700 ;23.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 767 ;12.132 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 50 ;15.067 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 672 ; 0.150 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3631 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2918 ; 1.417 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4624 ; 2.249 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1763 ; 3.659 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1722 ; 5.771 ; 4.500 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4YIM 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_1000207532. 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 : PH 6.5 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) : 1.1 REMARK 200 MONOCHROMATOR : NULL 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 : 117919 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 62.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.0800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 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: 4YIB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5-2.0 AMMONIUM SULFATE, PEG 400, 0.1 REMARK 280 M, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K 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 33.52400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.30250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.48300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.30250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.52400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.48300 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: 1260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 361 CG CD NE CZ NH1 NH2 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 PRO B 33 O HOH B 801 1.10 REMARK 500 OE2 GLU B 220 S SO4 B 704 1.11 REMARK 500 NH1 ARG B 55 O HOH B 802 1.11 REMARK 500 OE2 GLU B 220 O2 SO4 B 704 1.12 REMARK 500 OE1 GLU B 220 O1 SO4 B 704 1.28 REMARK 500 OE2 GLU B 220 O4 SO4 B 704 1.51 REMARK 500 O HOH B 1231 O HOH B 1686 1.60 REMARK 500 O HOH B 1235 O HOH B 1605 1.62 REMARK 500 O HOH B 1522 O HOH B 1552 1.63 REMARK 500 C PRO B 33 O HOH B 801 1.65 REMARK 500 CD GLU B 220 S SO4 B 704 1.66 REMARK 500 O HOH B 1257 O HOH B 1317 1.72 REMARK 500 NH1 ARG B 559 O HOH B 1642 1.75 REMARK 500 NZ LYS B 31 O HOH B 803 1.81 REMARK 500 O3 SO4 B 704 O HOH B 804 1.82 REMARK 500 CD GLU B 220 O4 SO4 B 704 1.84 REMARK 500 NH1 ARG B 343 CD2 LEU B 446 1.86 REMARK 500 NZ LYS B 369 O HOH B 805 1.89 REMARK 500 O HOH B 1488 O HOH B 1664 1.91 REMARK 500 O HOH B 891 O HOH B 1111 1.93 REMARK 500 OE1 GLU B 220 S SO4 B 704 1.98 REMARK 500 CD GLU B 220 O1 SO4 B 704 2.00 REMARK 500 CD GLU B 220 O2 SO4 B 704 2.02 REMARK 500 OE1 GLU B 98 O HOH B 1620 2.02 REMARK 500 NZ LYS B 31 O HOH B 806 2.03 REMARK 500 O HOH B 1338 O HOH B 1418 2.04 REMARK 500 O HOH B 1038 O HOH B 1639 2.04 REMARK 500 O HOH B 1569 O HOH B 1652 2.05 REMARK 500 O ALA B 40 O HOH B 807 2.06 REMARK 500 OE1 GLN B 489 O HOH B 808 2.06 REMARK 500 O HOH B 1253 O HOH B 1451 2.07 REMARK 500 O HOH B 1049 O HOH B 1078 2.07 REMARK 500 O HOH B 1527 O HOH B 1707 2.08 REMARK 500 O HOH B 1286 O HOH B 1473 2.11 REMARK 500 O HOH B 1309 O HOH B 1511 2.11 REMARK 500 O HOH B 1049 O HOH B 1579 2.11 REMARK 500 O HOH B 826 O HOH B 996 2.13 REMARK 500 O HOH B 874 O HOH B 1042 2.13 REMARK 500 O HOH B 1301 O HOH B 1604 2.13 REMARK 500 O HOH B 819 O HOH B 824 2.13 REMARK 500 O HOH B 1409 O HOH B 1667 2.14 REMARK 500 O ARG B 412 O HOH B 1471 2.14 REMARK 500 NH1 ARG B 136 O HOH B 809 2.14 REMARK 500 O HOH B 1452 O HOH B 1651 2.15 REMARK 500 O HOH B 1459 O HOH B 1672 2.16 REMARK 500 O HOH B 1253 O HOH B 1471 2.16 REMARK 500 O HOH B 1498 O HOH B 1603 2.17 REMARK 500 O HOH B 1079 O HOH B 1369 2.19 REMARK 500 O HOH B 1090 O HOH B 1121 2.19 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 B 929 O HOH B 940 3454 1.99 REMARK 500 O HOH B 1085 O HOH B 1113 3444 2.13 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 B 120 CG GLU B 120 CD 0.162 REMARK 500 GLU B 120 CD GLU B 120 OE1 0.176 REMARK 500 GLU B 120 CD GLU B 120 OE2 0.107 REMARK 500 SER B 135 CB SER B 135 OG -0.083 REMARK 500 TYR B 267 CD1 TYR B 267 CE1 0.114 REMARK 500 ARG B 408 CZ ARG B 408 NH1 0.093 REMARK 500 GLU B 568 CB GLU B 568 CG -0.138 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 ASP B 88 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG B 96 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 GLU B 120 CG - CD - OE2 ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG B 124 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP B 278 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 278 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 TYR B 284 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG B 290 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG B 290 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG B 320 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 322 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASP B 359 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP B 366 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 383 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASP B 396 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B 408 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 408 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 412 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG B 441 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG B 479 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 PHE B 578 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 582 NE - CZ - NH1 ANGL. DEV. = 4.0 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 B 186 63.58 -108.85 REMARK 500 THR B 205 -149.96 -119.65 REMARK 500 ARG B 343 78.01 -104.86 REMARK 500 THR B 459 -50.88 -122.10 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 B1258 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH B1440 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH B1535 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH B1537 DISTANCE = 7.15 ANGSTROMS REMARK 525 HOH B1540 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH B1584 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH B1588 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH B1591 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH B1643 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH B1646 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH B1647 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH B1657 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH B1661 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH B1665 DISTANCE = 6.25 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 707 DBREF 4YIM B 31 616 UNP Q9JXP1 Q9JXP1_NEIMB 31 616 SEQRES 1 B 586 LYS THR PRO ALA ASP ASN ILE GLU THR ALA ASP LEU SER SEQRES 2 B 586 ALA SER VAL PRO THR ARG PRO ALA GLU PRO GLU ARG LYS SEQRES 3 B 586 THR LEU ALA ASP TYR GLY GLY TYR PRO SER ALA LEU ASP SEQRES 4 B 586 ALA VAL LYS GLN LYS ASN ASP ALA ALA VAL ALA ALA TYR SEQRES 5 B 586 LEU GLU ASN ALA GLY ASP SER ALA MET ALA GLU ASN VAL SEQRES 6 B 586 ARG ASN GLU TRP LEU LYS SER LEU GLY ALA ARG ARG GLN SEQRES 7 B 586 TRP THR LEU PHE ALA GLN GLU TYR ALA LYS LEU GLU PRO SEQRES 8 B 586 ALA GLY ARG ALA GLN GLU VAL GLU CYS TYR ALA ASP SER SEQRES 9 B 586 SER ARG ASN ASP TYR THR ARG ALA ALA GLU LEU VAL LYS SEQRES 10 B 586 ASN THR GLY LYS LEU PRO SER GLY CYS THR LYS LEU LEU SEQRES 11 B 586 GLU GLN ALA ALA ALA SER GLY LEU LEU ASP GLY ASN ASP SEQRES 12 B 586 ALA TRP ARG ARG VAL ARG GLY LEU LEU ALA GLY ARG GLN SEQRES 13 B 586 THR THR ASP ALA ARG ASN LEU ALA ALA ALA LEU GLY SER SEQRES 14 B 586 PRO PHE ASP GLY GLY THR GLN GLY SER ARG GLU TYR ALA SEQRES 15 B 586 LEU LEU ASN VAL ILE GLY LYS GLU ALA ARG LYS SER PRO SEQRES 16 B 586 ASN ALA ALA ALA LEU LEU SER GLU MET GLU SER GLY LEU SEQRES 17 B 586 SER LEU GLU GLN ARG SER PHE ALA TRP GLY VAL LEU GLY SEQRES 18 B 586 HIS TYR GLN SER GLN ASN LEU ASN VAL PRO ALA ALA LEU SEQRES 19 B 586 ASP TYR TYR GLY LYS VAL ALA ASP ARG ARG GLN LEU THR SEQRES 20 B 586 ASP ASP GLN ILE GLU TRP TYR ALA ARG ALA ALA LEU ARG SEQRES 21 B 586 ALA ARG ARG TRP ASP GLU LEU ALA SER VAL ILE SER HIS SEQRES 22 B 586 MET PRO GLU LYS LEU GLN LYS SER PRO THR TRP LEU TYR SEQRES 23 B 586 TRP LEU ALA ARG SER ARG ALA ALA THR GLY ASN THR GLN SEQRES 24 B 586 GLU ALA GLU LYS LEU TYR LYS GLN ALA ALA ALA THR GLY SEQRES 25 B 586 ARG ASN PHE TYR ALA VAL LEU ALA GLY GLU GLU LEU GLY SEQRES 26 B 586 ARG LYS ILE ASP THR ARG ASN ASN VAL PRO ASP ALA GLY SEQRES 27 B 586 LYS ASN SER VAL ARG ARG MET ALA GLU ASP GLY ALA VAL SEQRES 28 B 586 LYS ARG ALA LEU VAL LEU PHE GLN ASN SER GLN SER ALA SEQRES 29 B 586 GLY ASP ALA LYS MET ARG ARG GLN ALA GLN ALA GLU TRP SEQRES 30 B 586 ARG PHE ALA THR ARG GLY PHE ASP GLU ASP LYS LEU LEU SEQRES 31 B 586 THR ALA ALA GLN THR ALA PHE ASP HIS GLY PHE TYR ASP SEQRES 32 B 586 MET ALA VAL ASN SER ALA GLU ARG THR ASP ARG LYS LEU SEQRES 33 B 586 ASN TYR THR LEU ARG TYR ILE SER PRO PHE LYS ASP THR SEQRES 34 B 586 VAL ILE ARG HIS ALA GLN ASN VAL ASN VAL ASP PRO ALA SEQRES 35 B 586 TRP VAL TYR GLY LEU ILE ARG GLN GLU SER ARG PHE VAL SEQRES 36 B 586 ILE GLY ALA GLN SER ARG VAL GLY ALA GLN GLY LEU MET SEQRES 37 B 586 GLN VAL MET PRO ALA THR ALA ARG GLU ILE ALA GLY LYS SEQRES 38 B 586 ILE GLY MET ASP ALA ALA GLN LEU TYR THR ALA ASP GLY SEQRES 39 B 586 ASN ILE ARG MET GLY THR TRP TYR MET ALA ASP THR LYS SEQRES 40 B 586 ARG ARG LEU GLN ASN ASN GLU VAL LEU ALA THR ALA GLY SEQRES 41 B 586 TYR ASN ALA GLY PRO GLY ARG ALA ARG ARG TRP GLN ALA SEQRES 42 B 586 ASP THR PRO LEU GLU GLY ALA VAL TYR ALA GLU THR ILE SEQRES 43 B 586 PRO PHE SER GLU THR ARG ASP TYR VAL LYS LYS VAL MET SEQRES 44 B 586 ALA ASN ALA ALA TYR TYR ALA ALA LEU PHE GLY ALA PRO SEQRES 45 B 586 HIS ILE PRO LEU LYS GLN ARG MET GLY ILE VAL PRO ALA SEQRES 46 B 586 ARG HET SO4 B 701 5 HET SO4 B 702 5 HET SO4 B 703 5 HET SO4 B 704 5 HET SO4 B 705 5 HET SO4 B 706 5 HET SO4 B 707 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 7(O4 S 2-) FORMUL 9 HOH *912(H2 O) HELIX 1 AA1 THR B 32 ASN B 36 5 5 HELIX 2 AA2 PRO B 53 GLN B 73 1 21 HELIX 3 AA3 ASN B 75 ASN B 85 1 11 HELIX 4 AA4 SER B 89 ARG B 106 1 18 HELIX 5 AA5 GLN B 108 ALA B 117 1 10 HELIX 6 AA6 LYS B 118 LEU B 119 5 2 HELIX 7 AA7 GLU B 120 ARG B 124 5 5 HELIX 8 AA8 ALA B 125 ARG B 136 1 12 HELIX 9 AA9 ARG B 141 VAL B 146 1 6 HELIX 10 AB1 PRO B 153 SER B 166 1 14 HELIX 11 AB2 ASP B 170 GLY B 184 1 15 HELIX 12 AB3 GLN B 186 LEU B 197 1 12 HELIX 13 AB4 THR B 205 LEU B 213 1 9 HELIX 14 AB5 LEU B 213 GLY B 218 1 6 HELIX 15 AB6 GLU B 220 SER B 224 5 5 HELIX 16 AB7 ASN B 226 GLU B 235 1 10 HELIX 17 AB8 SER B 236 LEU B 238 5 3 HELIX 18 AB9 SER B 239 ASN B 257 1 19 HELIX 19 AC1 ASN B 259 LYS B 269 1 11 HELIX 20 AC2 ASP B 272 LEU B 276 5 5 HELIX 21 AC3 THR B 277 ALA B 291 1 15 HELIX 22 AC4 ARG B 293 HIS B 303 1 11 HELIX 23 AC5 PRO B 305 LYS B 310 1 6 HELIX 24 AC6 SER B 311 THR B 325 1 15 HELIX 25 AC7 ASN B 327 ALA B 340 1 14 HELIX 26 AC8 ASN B 344 LEU B 354 1 11 HELIX 27 AC9 GLY B 368 ASP B 378 1 11 HELIX 28 AD1 ASP B 378 GLY B 395 1 18 HELIX 29 AD2 ASP B 396 ARG B 412 1 17 HELIX 30 AD3 ASP B 415 HIS B 429 1 15 HELIX 31 AD4 PHE B 431 ARG B 441 1 11 HELIX 32 AD5 ASN B 447 TYR B 452 1 6 HELIX 33 AD6 PHE B 456 VAL B 467 1 12 HELIX 34 AD7 ASP B 470 ARG B 483 1 14 HELIX 35 AD8 MET B 501 GLY B 513 1 13 HELIX 36 AD9 ASP B 515 TYR B 520 5 6 HELIX 37 AE1 THR B 521 LEU B 540 1 20 HELIX 38 AE2 ASN B 543 GLY B 554 1 12 HELIX 39 AE3 GLY B 554 TRP B 561 1 8 HELIX 40 AE4 GLY B 569 THR B 575 1 7 HELIX 41 AE5 PHE B 578 GLY B 600 1 23 HELIX 42 AE6 PRO B 605 GLY B 611 1 7 SHEET 1 AA1 2 LEU B 567 GLU B 568 0 SHEET 2 AA1 2 ILE B 612 VAL B 613 -1 O VAL B 613 N LEU B 567 SSBOND 1 CYS B 130 CYS B 156 1555 1555 2.43 SITE 1 AC1 11 GLY B 342 ARG B 343 GLU B 440 THR B 442 SITE 2 AC1 11 ARG B 451 HOH B1211 HOH B1263 HOH B1522 SITE 3 AC1 11 HOH B1552 HOH B1553 HOH B1561 SITE 1 AC2 14 GLY B 368 LYS B 369 ASN B 370 SER B 371 SITE 2 AC2 14 ASN B 468 LYS B 537 ASN B 542 HOH B 823 SITE 3 AC2 14 HOH B 825 HOH B 837 HOH B 910 HOH B 942 SITE 4 AC2 14 HOH B 974 HOH B 979 SITE 1 AC3 9 ARG B 479 ARG B 483 LYS B 587 HOH B1133 SITE 2 AC3 9 HOH B1212 HOH B1220 HOH B1345 HOH B1522 SITE 3 AC3 9 HOH B1541 SITE 1 AC4 8 ASN B 36 ARG B 185 GLY B 218 LYS B 219 SITE 2 AC4 8 GLU B 220 ALA B 221 HOH B 804 HOH B 887 SITE 1 AC5 5 PRO B 53 GLU B 54 LYS B 382 HOH B1000 SITE 2 AC5 5 HOH B1215 SITE 1 AC6 5 GLN B 206 ARG B 209 GLN B 242 HOH B1348 SITE 2 AC6 5 HOH B1574 SITE 1 AC7 6 ALA B 125 GLN B 126 HOH B1196 HOH B1321 SITE 2 AC7 6 HOH B1544 HOH B1638 CRYST1 67.048 72.966 124.605 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 0.014915 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008025 0.00000