HEADER HYDROLASE 02-APR-09 3GXK TITLE THE CRYSTAL STRUCTURE OF G-TYPE LYSOZYME FROM ATLANTIC COD (GADUS TITLE 2 MORHUA L.) IN COMPLEX WITH NAG OLIGOMERS SHEDS NEW LIGHT ON SUBSTRATE TITLE 3 BINDING AND THE CATALYTIC MECHANISM. NATIVE STRUCTURE TO 1.9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOOSE-TYPE LYSOZYME 1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 31-217; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GADUS MORHUA; SOURCE 3 ORGANISM_COMMON: ATLANTIC COD; SOURCE 4 ORGANISM_TAXID: 8049; SOURCE 5 GENE: LYSOZYME; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 STAR (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET151/D-TOPO GLYS KEYWDS ATLANTIC COD, FISH LYSOZYME, ACTIVE SITE RESIDUES, SUBSTRATE BINDING KEYWDS 2 SITES, SURFACE POTENTIAL, MURAMIDASE ACTIVITY, IMMUNE SYSTEM, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.HELLAND,R.L.LARSEN,S.FINSTAD,P.KYOMUHENDO,A.N.LARSEN REVDAT 2 01-NOV-17 3GXK 1 REMARK REVDAT 1 20-OCT-09 3GXK 0 JRNL AUTH R.HELLAND,R.L.LARSEN,S.FINSTAD,P.KYOMUHENDO,A.N.LARSEN JRNL TITL CRYSTAL STRUCTURES OF G-TYPE LYSOZYME FROM ATLANTIC COD SHED JRNL TITL 2 NEW LIGHT ON SUBSTRATE BINDING AND THE CATALYTIC MECHANISM. JRNL REF CELL.MOL.LIFE SCI. V. 66 2585 2009 JRNL REFN ISSN 1420-682X JRNL PMID 19543850 JRNL DOI 10.1007/S00018-009-0063-X REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0021 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 47647 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2548 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3279 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 187 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5731 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 257 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.53000 REMARK 3 B22 (A**2) : -0.79000 REMARK 3 B33 (A**2) : 0.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.58000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.827 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5848 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7899 ; 1.563 ; 1.920 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 723 ; 6.108 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 298 ;36.841 ;24.329 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 986 ;16.314 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;20.667 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 826 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4543 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2955 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4078 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 310 ; 0.166 ; 0.200 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): 90 ; 0.219 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.187 ; 0.200 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): 3750 ; 1.083 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5759 ; 1.646 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2520 ; 2.658 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2140 ; 3.895 ; 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 : 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 3GXK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50202 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.22100 REMARK 200 R SYM FOR SHELL (I) : 0.22100 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 154L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 48-53% AMMONIUM SULPHATE, 5MM COCL2, REMARK 280 0.1M BISTRIS, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 55.06000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.06000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.69500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 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 HOH B 246 LIES ON A SPECIAL POSITION. 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 VAL A 3 REMARK 465 GLY A 4 REMARK 465 VAL B 3 REMARK 465 GLY B 4 REMARK 465 TYR B 5 REMARK 465 GLY B 6 REMARK 465 VAL C 79 REMARK 465 ILE C 80 REMARK 465 PHE C 81 REMARK 465 ASN C 82 REMARK 465 THR C 83 REMARK 465 THR C 84 REMARK 465 PRO C 85 REMARK 465 PRO C 86 REMARK 465 GLY C 87 REMARK 465 TRP C 88 REMARK 465 GLY C 89 REMARK 465 ASP C 90 REMARK 465 ASN C 91 REMARK 465 VAL D 3 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 NH1 ARG C 44 O ARG C 75 2.01 REMARK 500 CB ASN A 126 O HOH A 248 2.16 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 OE2 GLU B 159 OE2 GLU B 159 2656 1.96 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 C 106 CD GLU C 106 OE2 0.068 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 B 44 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 44 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG D 180 NE - CZ - NH1 ANGL. DEV. = 3.5 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 29 -159.10 -128.16 REMARK 500 ASP A 172 20.28 -151.50 REMARK 500 ASP B 29 -159.02 -134.53 REMARK 500 ASP B 172 12.71 -154.83 REMARK 500 TYR C 5 -4.23 60.55 REMARK 500 ASP C 29 -166.11 -126.42 REMARK 500 ASP C 172 14.98 -155.79 REMARK 500 ASP D 29 -158.96 -129.31 REMARK 500 PHE D 135 63.52 -115.80 REMARK 500 ASP D 172 17.74 -156.27 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 ASP A 90 ASN A 91 -47.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GXR RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE DISCREPANCY FROM THE DEPOSITED UNIPROT SEQUENCE IS DUE TO REMARK 999 ALLELIC VARIATION OF THE GENE. DBREF 3GXK A 3 189 UNP B9TU22 B9TU22_GADMO 31 217 DBREF 3GXK B 3 189 UNP B9TU22 B9TU22_GADMO 31 217 DBREF 3GXK C 3 189 UNP B9TU22 B9TU22_GADMO 31 217 DBREF 3GXK D 3 189 UNP B9TU22 B9TU22_GADMO 31 217 SEQADV 3GXK ALA A 147 UNP B9TU22 GLY 175 SEE REMARK 999 SEQADV 3GXK ALA B 147 UNP B9TU22 GLY 175 SEE REMARK 999 SEQADV 3GXK ALA C 147 UNP B9TU22 GLY 175 SEE REMARK 999 SEQADV 3GXK ALA D 147 UNP B9TU22 GLY 175 SEE REMARK 999 SEQRES 1 A 187 VAL GLY TYR GLY ASP ILE THR GLN VAL GLU THR SER GLY SEQRES 2 A 187 ALA SER SER LYS THR SER ARG GLN ASP LYS LEU GLU TYR SEQRES 3 A 187 ASP GLY VAL ARG ALA SER HIS THR MET ALA GLN THR ASP SEQRES 4 A 187 ALA GLY ARG MET GLU LYS TYR LYS SER PHE ILE ASN ASN SEQRES 5 A 187 VAL ALA LYS LYS HIS VAL VAL ASP PRO ALA VAL ILE ALA SEQRES 6 A 187 ALA ILE ILE SER ARG GLU SER ARG ALA GLY ASN VAL ILE SEQRES 7 A 187 PHE ASN THR THR PRO PRO GLY TRP GLY ASP ASN TYR ASN SEQRES 8 A 187 GLY PHE GLY LEU MET GLN VAL ASP LYS ARG TYR HIS GLU SEQRES 9 A 187 PRO ARG GLY ALA TRP ASN SER GLU GLU HIS ILE ASP GLN SEQRES 10 A 187 ALA THR GLY ILE LEU VAL ASN PHE ILE GLN LEU ILE GLN SEQRES 11 A 187 LYS LYS PHE PRO SER TRP SER THR GLU GLN GLN LEU LYS SEQRES 12 A 187 GLY ALA ILE ALA ALA TYR ASN THR GLY ASP GLY ARG VAL SEQRES 13 A 187 GLU SER TYR GLU SER VAL ASP SER ARG THR THR GLY LYS SEQRES 14 A 187 ASP TYR SER ASN ASP VAL VAL ALA ARG ALA GLN TRP TYR SEQRES 15 A 187 LYS LYS ASN GLY PHE SEQRES 1 B 187 VAL GLY TYR GLY ASP ILE THR GLN VAL GLU THR SER GLY SEQRES 2 B 187 ALA SER SER LYS THR SER ARG GLN ASP LYS LEU GLU TYR SEQRES 3 B 187 ASP GLY VAL ARG ALA SER HIS THR MET ALA GLN THR ASP SEQRES 4 B 187 ALA GLY ARG MET GLU LYS TYR LYS SER PHE ILE ASN ASN SEQRES 5 B 187 VAL ALA LYS LYS HIS VAL VAL ASP PRO ALA VAL ILE ALA SEQRES 6 B 187 ALA ILE ILE SER ARG GLU SER ARG ALA GLY ASN VAL ILE SEQRES 7 B 187 PHE ASN THR THR PRO PRO GLY TRP GLY ASP ASN TYR ASN SEQRES 8 B 187 GLY PHE GLY LEU MET GLN VAL ASP LYS ARG TYR HIS GLU SEQRES 9 B 187 PRO ARG GLY ALA TRP ASN SER GLU GLU HIS ILE ASP GLN SEQRES 10 B 187 ALA THR GLY ILE LEU VAL ASN PHE ILE GLN LEU ILE GLN SEQRES 11 B 187 LYS LYS PHE PRO SER TRP SER THR GLU GLN GLN LEU LYS SEQRES 12 B 187 GLY ALA ILE ALA ALA TYR ASN THR GLY ASP GLY ARG VAL SEQRES 13 B 187 GLU SER TYR GLU SER VAL ASP SER ARG THR THR GLY LYS SEQRES 14 B 187 ASP TYR SER ASN ASP VAL VAL ALA ARG ALA GLN TRP TYR SEQRES 15 B 187 LYS LYS ASN GLY PHE SEQRES 1 C 187 VAL GLY TYR GLY ASP ILE THR GLN VAL GLU THR SER GLY SEQRES 2 C 187 ALA SER SER LYS THR SER ARG GLN ASP LYS LEU GLU TYR SEQRES 3 C 187 ASP GLY VAL ARG ALA SER HIS THR MET ALA GLN THR ASP SEQRES 4 C 187 ALA GLY ARG MET GLU LYS TYR LYS SER PHE ILE ASN ASN SEQRES 5 C 187 VAL ALA LYS LYS HIS VAL VAL ASP PRO ALA VAL ILE ALA SEQRES 6 C 187 ALA ILE ILE SER ARG GLU SER ARG ALA GLY ASN VAL ILE SEQRES 7 C 187 PHE ASN THR THR PRO PRO GLY TRP GLY ASP ASN TYR ASN SEQRES 8 C 187 GLY PHE GLY LEU MET GLN VAL ASP LYS ARG TYR HIS GLU SEQRES 9 C 187 PRO ARG GLY ALA TRP ASN SER GLU GLU HIS ILE ASP GLN SEQRES 10 C 187 ALA THR GLY ILE LEU VAL ASN PHE ILE GLN LEU ILE GLN SEQRES 11 C 187 LYS LYS PHE PRO SER TRP SER THR GLU GLN GLN LEU LYS SEQRES 12 C 187 GLY ALA ILE ALA ALA TYR ASN THR GLY ASP GLY ARG VAL SEQRES 13 C 187 GLU SER TYR GLU SER VAL ASP SER ARG THR THR GLY LYS SEQRES 14 C 187 ASP TYR SER ASN ASP VAL VAL ALA ARG ALA GLN TRP TYR SEQRES 15 C 187 LYS LYS ASN GLY PHE SEQRES 1 D 187 VAL GLY TYR GLY ASP ILE THR GLN VAL GLU THR SER GLY SEQRES 2 D 187 ALA SER SER LYS THR SER ARG GLN ASP LYS LEU GLU TYR SEQRES 3 D 187 ASP GLY VAL ARG ALA SER HIS THR MET ALA GLN THR ASP SEQRES 4 D 187 ALA GLY ARG MET GLU LYS TYR LYS SER PHE ILE ASN ASN SEQRES 5 D 187 VAL ALA LYS LYS HIS VAL VAL ASP PRO ALA VAL ILE ALA SEQRES 6 D 187 ALA ILE ILE SER ARG GLU SER ARG ALA GLY ASN VAL ILE SEQRES 7 D 187 PHE ASN THR THR PRO PRO GLY TRP GLY ASP ASN TYR ASN SEQRES 8 D 187 GLY PHE GLY LEU MET GLN VAL ASP LYS ARG TYR HIS GLU SEQRES 9 D 187 PRO ARG GLY ALA TRP ASN SER GLU GLU HIS ILE ASP GLN SEQRES 10 D 187 ALA THR GLY ILE LEU VAL ASN PHE ILE GLN LEU ILE GLN SEQRES 11 D 187 LYS LYS PHE PRO SER TRP SER THR GLU GLN GLN LEU LYS SEQRES 12 D 187 GLY ALA ILE ALA ALA TYR ASN THR GLY ASP GLY ARG VAL SEQRES 13 D 187 GLU SER TYR GLU SER VAL ASP SER ARG THR THR GLY LYS SEQRES 14 D 187 ASP TYR SER ASN ASP VAL VAL ALA ARG ALA GLN TRP TYR SEQRES 15 D 187 LYS LYS ASN GLY PHE HET CO B 200 1 HET CO C 200 1 HETNAM CO COBALT (II) ION FORMUL 5 CO 2(CO 2+) FORMUL 7 HOH *257(H2 O) HELIX 1 1 ASP A 7 VAL A 11 5 5 HELIX 2 2 SER A 17 ASP A 24 1 8 HELIX 3 3 ASP A 29 GLU A 46 1 18 HELIX 4 4 TYR A 48 VAL A 60 1 13 HELIX 5 5 ASP A 62 ARG A 75 1 14 HELIX 6 6 SER A 113 PHE A 135 1 23 HELIX 7 7 SER A 139 GLY A 154 1 16 HELIX 8 8 ASP A 155 VAL A 158 5 4 HELIX 9 9 THR A 168 LYS A 171 5 4 HELIX 10 10 ASP A 172 GLY A 188 1 17 HELIX 11 11 ASP B 7 VAL B 11 5 5 HELIX 12 12 SER B 17 ARG B 22 1 6 HELIX 13 13 GLN B 23 LYS B 25 5 3 HELIX 14 14 ASP B 29 GLU B 46 1 18 HELIX 15 15 TYR B 48 VAL B 60 1 13 HELIX 16 16 ASP B 62 ARG B 75 1 14 HELIX 17 17 ALA B 76 ASN B 78 5 3 HELIX 18 18 SER B 113 PHE B 135 1 23 HELIX 19 19 SER B 139 GLY B 154 1 16 HELIX 20 20 ASP B 155 VAL B 158 5 4 HELIX 21 21 THR B 168 LYS B 171 5 4 HELIX 22 22 ASP B 172 LYS B 186 1 15 HELIX 23 23 ASP C 7 VAL C 11 5 5 HELIX 24 24 SER C 17 ARG C 22 1 6 HELIX 25 25 GLN C 23 LYS C 25 5 3 HELIX 26 26 ASP C 29 GLU C 46 1 18 HELIX 27 27 TYR C 48 VAL C 60 1 13 HELIX 28 28 ASP C 62 ARG C 75 1 14 HELIX 29 29 SER C 113 PHE C 135 1 23 HELIX 30 30 SER C 139 GLY C 154 1 16 HELIX 31 31 ASP C 155 VAL C 158 5 4 HELIX 32 32 THR C 168 LYS C 171 5 4 HELIX 33 33 ASP C 172 LYS C 186 1 15 HELIX 34 34 ASP D 7 VAL D 11 5 5 HELIX 35 35 SER D 17 ARG D 22 1 6 HELIX 36 36 GLN D 23 LYS D 25 5 3 HELIX 37 37 ASP D 29 GLU D 46 1 18 HELIX 38 38 TYR D 48 VAL D 60 1 13 HELIX 39 39 ASP D 62 ARG D 75 1 14 HELIX 40 40 SER D 113 PHE D 135 1 23 HELIX 41 41 SER D 139 GLY D 154 1 16 HELIX 42 42 ASP D 155 VAL D 158 5 4 HELIX 43 43 THR D 168 LYS D 171 5 4 HELIX 44 44 ASP D 172 LYS D 186 1 15 SHEET 1 A 3 TRP A 88 GLY A 89 0 SHEET 2 A 3 GLY A 94 PHE A 95 -1 O GLY A 94 N GLY A 89 SHEET 3 A 3 VAL A 100 ASP A 101 -1 O VAL A 100 N PHE A 95 SHEET 1 B 3 TRP B 88 GLY B 89 0 SHEET 2 B 3 GLY B 94 PHE B 95 -1 O GLY B 94 N GLY B 89 SHEET 3 B 3 VAL B 100 ASP B 101 -1 O VAL B 100 N PHE B 95 SHEET 1 C 2 GLY C 94 PHE C 95 0 SHEET 2 C 2 VAL C 100 ASP C 101 -1 O VAL C 100 N PHE C 95 SHEET 1 D 3 TRP D 88 GLY D 89 0 SHEET 2 D 3 GLY D 94 PHE D 95 -1 O GLY D 94 N GLY D 89 SHEET 3 D 3 VAL D 100 ASP D 101 -1 O VAL D 100 N PHE D 95 CISPEP 1 THR A 84 PRO A 85 0 -3.17 CISPEP 2 THR B 84 PRO B 85 0 -0.13 CISPEP 3 GLY C 4 TYR C 5 0 3.34 CISPEP 4 GLY D 4 TYR D 5 0 3.32 CISPEP 5 THR D 84 PRO D 85 0 -10.44 SITE 1 AC1 2 GLU A 106 HIS B 35 SITE 1 AC2 2 HIS C 35 GLU D 106 CRYST1 110.120 75.390 78.370 90.00 92.92 90.00 C 1 2 1 16 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 0.009081 0.000000 0.000464 0.00000 SCALE2 0.000000 0.013264 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012777 0.00000 MASTER 414 0 2 44 11 0 2 6 0 0 0 60 END