PDB Short entry for 4II9 HEADER TRANSFERASE/PEPTIDE/RNA 20-DEC-12 4II9 TITLE CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO TITLE 2 ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-RNA CONJUGATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FEMX; COMPND 3 CHAIN: A; COMPND 4 EC: 2.3.2.10; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5-MER PEPTIDE; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: RNA (5'-R(P*CP*CP*(A9Z))-3'); COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: WEISSELLA VIRIDESCENS; SOURCE 3 ORGANISM_TAXID: 1629; SOURCE 4 STRAIN: CIP102810T; SOURCE 5 GENE: FEMX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TOP10; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTRC-HIS60; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC PEPTIDE; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS FEMX, PEPTIDOGLYCAN, TRANSFERASE, PEPTIDYL-RNA CONJUGATE COMPLEX, KEYWDS 2 TRANSFERASE-PEPTIDE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.LI DE LA SIERRA-GALLAY,M.FONVIELLE,H.VAN TILBEURGH,M.ARTHUR, AUTHOR 2 M.ETHEVE-QUELQUEJEU REVDAT 4 08-NOV-23 4II9 1 HETSYN REVDAT 3 29-JUL-20 4II9 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 07-AUG-13 4II9 1 JRNL REVDAT 1 03-JUL-13 4II9 0 JRNL AUTH M.FONVIELLE,I.LI DE LA SIERRA-GALLAY,A.H.EL-SAGHEER, JRNL AUTH 2 M.LECERF,D.PATIN,D.MELLAL,C.MAYER,D.BLANOT,N.GALE,T.BROWN, JRNL AUTH 3 H.VAN TILBEURGH,M.ETHEVE-QUELQUEJEU,M.ARTHUR JRNL TITL THE STRUCTURE OF FEMXWV IN COMPLEX WITH A PEPTIDYL-RNA JRNL TITL 2 CONJUGATE: MECHANISM OF AMINOACYL TRANSFER FROM JRNL TITL 3 ALA-TRNA(ALA) TO PEPTIDOGLYCAN PRECURSORS JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 52 7278 2013 JRNL REFN ISSN 1433-7851 JRNL PMID 23744707 JRNL DOI 10.1002/ANIE.201301411 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 42482 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2236 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) : 1.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3011 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2727 REMARK 3 NUCLEIC ACID ATOMS : 68 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.95000 REMARK 3 B22 (A**2) : -1.07000 REMARK 3 B33 (A**2) : 1.75000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.41000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.632 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2924 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3978 ; 2.342 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 5.842 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;33.099 ;24.388 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 466 ;12.135 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;21.742 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 436 ; 0.170 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2209 ; 0.013 ; 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): 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4II9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076785. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.9791 REMARK 200 MONOCHROMATOR : CHANNEL CUT CRYOGENICALLY COOLED REMARK 200 MONOCHROMATOR CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44718 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 38.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.18900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3GKR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-SODIUM CITRATE BUFFER, 0.2M REMARK 280 AMMONIUM ACETATE, 33% POLYETHYLENE GLYCOL 4K, PH 5.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 50.88500 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 MET A 0 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 HIS A 341 REMARK 465 HIS A 342 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 HIS A 337 CG ND1 CD2 CE1 NE2 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 THR A 64 O HOH A 573 2.17 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 TRP A 278 CE2 TRP A 278 CD2 0.082 REMARK 500 C C 9 O3' A9Z C 10 P 0.119 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 23 CG - CD1 - CE1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ASP A 88 CB - CG - OD1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 LEU A 90 CB - CG - CD2 ANGL. DEV. = -12.5 DEGREES REMARK 500 ARG A 101 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 MET A 202 CA - CB - CG ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG A 211 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 C C 9 C3' - O3' - P ANGL. DEV. = -12.0 DEGREES REMARK 500 A9Z C 10 O3' - P - OP1 ANGL. DEV. = 10.8 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 MET A 79 -178.19 172.16 REMARK 500 ASN A 130 -102.40 -151.32 REMARK 500 LEU A 240 -54.20 -120.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NE9 RELATED DB: PDB REMARK 900 APO-FORM STRUCTURE REMARK 900 RELATED ID: 1P4N RELATED DB: PDB REMARK 900 PROTEIN-SUBSTRATE COMPLEX REMARK 900 RELATED ID: 1XE4 RELATED DB: PDB REMARK 900 K36M MUTANT REMARK 900 RELATED ID: 1XF8 RELATED DB: PDB REMARK 900 Y254 MUTANT REMARK 900 RELATED ID: 1XIX RELATED DB: PDB REMARK 900 APO FORM STRUCTURE FORM II REMARK 900 RELATED ID: 3GKR RELATED DB: PDB REMARK 900 PROTEIN-SUBSTRATE PRODUCT COMPLEX DBREF 4II9 A 0 335 UNP Q9EY50 Q9EY50_LACVI 1 336 DBREF 4II9 B 3 7 PDB 4II9 4II9 3 7 DBREF 4II9 C 8 10 PDB 4II9 4II9 8 10 SEQADV 4II9 GLY A 336 UNP Q9EY50 EXPRESSION TAG SEQADV 4II9 HIS A 337 UNP Q9EY50 EXPRESSION TAG SEQADV 4II9 HIS A 338 UNP Q9EY50 EXPRESSION TAG SEQADV 4II9 HIS A 339 UNP Q9EY50 EXPRESSION TAG SEQADV 4II9 HIS A 340 UNP Q9EY50 EXPRESSION TAG SEQADV 4II9 HIS A 341 UNP Q9EY50 EXPRESSION TAG SEQADV 4II9 HIS A 342 UNP Q9EY50 EXPRESSION TAG SEQRES 1 A 343 MET PRO VAL LEU ASN LEU ASN ASP PRO GLN ALA VAL GLU SEQRES 2 A 343 ARG TYR GLU GLU PHE MET ARG GLN SER PRO TYR GLY GLN SEQRES 3 A 343 VAL THR GLN ASP LEU GLY TRP ALA LYS VAL LYS ASN ASN SEQRES 4 A 343 TRP GLU PRO VAL ASP VAL TYR LEU GLU ASP ASP GLN GLY SEQRES 5 A 343 ALA ILE ILE ALA ALA MET SER MET LEU LEU GLY ASP THR SEQRES 6 A 343 PRO THR ASP LYS LYS PHE ALA TYR ALA SER LYS GLY PRO SEQRES 7 A 343 VAL MET ASP VAL THR ASP VAL ASP LEU LEU ASP ARG LEU SEQRES 8 A 343 VAL ASP GLU ALA VAL LYS ALA LEU ASP GLY ARG ALA TYR SEQRES 9 A 343 VAL LEU ARG PHE ASP PRO GLU VAL ALA TYR SER ASP GLU SEQRES 10 A 343 PHE ASN THR THR LEU GLN ASP HIS GLY TYR VAL THR ARG SEQRES 11 A 343 ASN ARG ASN VAL ALA ASP ALA GLY MET HIS ALA THR ILE SEQRES 12 A 343 GLN PRO ARG LEU ASN MET VAL LEU ASP LEU THR LYS PHE SEQRES 13 A 343 PRO ASP ALA LYS THR THR LEU ASP LEU TYR PRO SER LYS SEQRES 14 A 343 THR LYS SER LYS ILE LYS ARG PRO PHE ARG ASP GLY VAL SEQRES 15 A 343 GLU VAL HIS SER GLY ASN SER ALA THR GLU LEU ASP GLU SEQRES 16 A 343 PHE PHE LYS THR TYR THR THR MET ALA GLU ARG HIS GLY SEQRES 17 A 343 ILE THR HIS ARG PRO ILE GLU TYR PHE GLN ARG MET GLN SEQRES 18 A 343 ALA ALA PHE ASP ALA ASP THR MET ARG ILE PHE VAL ALA SEQRES 19 A 343 GLU ARG GLU GLY LYS LEU LEU SER THR GLY ILE ALA LEU SEQRES 20 A 343 LYS TYR GLY ARG LYS ILE TRP TYR MET TYR ALA GLY SER SEQRES 21 A 343 MET ASP GLY ASN THR TYR TYR ALA PRO TYR ALA VAL GLN SEQRES 22 A 343 SER GLU MET ILE GLN TRP ALA LEU ASP THR ASN THR ASP SEQRES 23 A 343 LEU TYR ASP LEU GLY GLY ILE GLU SER GLU SER THR ASP SEQRES 24 A 343 ASP SER LEU TYR VAL PHE LYS HIS VAL PHE VAL LYS ASP SEQRES 25 A 343 ALA PRO ARG GLU TYR ILE GLY GLU ILE ASP LYS VAL LEU SEQRES 26 A 343 ASP PRO GLU VAL TYR ALA GLU LEU VAL LYS ASP GLY HIS SEQRES 27 A 343 HIS HIS HIS HIS HIS SEQRES 1 B 5 ALA FGA CYS DAL DAL SEQRES 1 C 3 C C A9Z MODRES 4II9 A9Z C 10 A HET FGA B 4 9 HET DAL B 6 5 HET DAL B 7 6 HET A9Z C 10 28 HET GOL A 402 6 HET UDP B 101 24 HET MUB B 102 19 HETNAM FGA GAMMA-D-GLUTAMIC ACID HETNAM DAL D-ALANINE HETNAM A9Z 2'-DEOXY-2'-(4-ETHYL-1H-1,2,3-TRIAZOL-1-YL)ADENOSINE HETNAM 2 A9Z 5'-(DIHYDROGEN PHOSPHATE) HETNAM GOL GLYCEROL HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM MUB N-ACETYL-ALPHA-MURAMIC ACID HETSYN FGA D-GLUTAMIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN MUB N-ACETYL-MURAMIC ACID; N-ACETYLMURAMIC ACID FORMUL 2 FGA C5 H9 N O4 FORMUL 2 DAL 2(C3 H7 N O2) FORMUL 3 A9Z C14 H19 N8 O6 P FORMUL 4 GOL C3 H8 O3 FORMUL 5 UDP C9 H14 N2 O12 P2 FORMUL 6 MUB C11 H19 N O8 FORMUL 7 HOH *296(H2 O) HELIX 1 1 ASP A 7 SER A 21 1 15 HELIX 2 2 GLN A 25 ASP A 29 5 5 HELIX 3 3 LEU A 30 LYS A 36 1 7 HELIX 4 4 ASP A 83 ASP A 99 1 17 HELIX 5 5 SER A 114 HIS A 124 1 11 HELIX 6 6 VAL A 133 THR A 141 5 9 HELIX 7 7 THR A 153 PHE A 155 5 3 HELIX 8 8 THR A 160 TYR A 165 5 6 HELIX 9 9 PRO A 166 ASP A 179 1 14 HELIX 10 10 SER A 188 GLY A 207 1 20 HELIX 11 11 PRO A 212 PHE A 223 1 12 HELIX 12 12 TYR A 266 THR A 282 1 17 HELIX 13 13 ASP A 299 VAL A 309 1 11 HELIX 14 14 ASP A 325 VAL A 333 1 9 SHEET 1 A 6 GLU A 40 GLU A 47 0 SHEET 2 A 6 ILE A 53 GLY A 62 -1 O MET A 57 N VAL A 44 SHEET 3 A 6 LYS A 69 ALA A 73 -1 O PHE A 70 N GLY A 62 SHEET 4 A 6 ALA A 102 PHE A 107 1 O ARG A 106 N ALA A 73 SHEET 5 A 6 GLU A 319 VAL A 323 -1 O LYS A 322 N LEU A 105 SHEET 6 A 6 VAL A 127 ARG A 129 -1 N VAL A 127 O ASP A 321 SHEET 1 B 7 VAL A 181 GLY A 186 0 SHEET 2 B 7 MET A 228 ARG A 235 -1 O VAL A 232 N HIS A 184 SHEET 3 B 7 LYS A 238 TYR A 248 -1 O GLY A 243 N PHE A 231 SHEET 4 B 7 LYS A 251 SER A 259 -1 O TRP A 253 N LEU A 246 SHEET 5 B 7 LEU A 286 ILE A 292 1 O ASP A 288 N TYR A 254 SHEET 6 B 7 LEU A 146 ASP A 151 -1 N LEU A 150 O TYR A 287 SHEET 7 B 7 ARG A 314 GLU A 315 -1 O ARG A 314 N ASN A 147 LINK C ALA B 3 N FGA B 4 1555 1555 1.35 LINK N ALA B 3 C10 MUB B 102 1555 1555 1.38 LINK CD FGA B 4 N CYS B 5 1555 1555 1.41 LINK C CYS B 5 N DAL B 6 1555 1555 1.34 LINK SG CYS B 5 C7T A9Z C 10 1555 1555 1.79 LINK C DAL B 6 N DAL B 7 1555 1555 1.36 LINK PB UDP B 101 O1 MUB B 102 1555 1555 1.62 LINK O3' C C 9 P A9Z C 10 1555 1555 1.73 CISPEP 1 GLY A 76 PRO A 77 0 0.46 CRYST1 42.130 101.770 46.320 90.00 102.60 90.00 P 1 21 1 2 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 0.023736 0.000000 0.005306 0.00000 SCALE2 0.000000 0.009826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022122 0.00000