HEADER TRANSFERASE/TRANSFERASE PRODUCT 11-MAR-09 3GKR TITLE CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMX:UDP-MURNAC-HEXAPEPTIDE TITLE 2 COMPLEX 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: UDP-MURNAC-PEPTIDE; COMPND 8 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS VIRIDESCENS; SOURCE 3 ORGANISM_TAXID: 1629; SOURCE 4 GENE: FEMX; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTYB2; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 12 ORGANISM_TAXID: 1280 KEYWDS FEMX, PEPTIDOGLYCAN, HEXAPEPTIDE, TRANSFERASE, TRANSFERASE- KEYWDS 2 TRANSFERASE PRODUCT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.DELFOSSE,J.PITON,R.VILLET,M.LECERF,M.ARTHUR,C.MAYER REVDAT 5 01-NOV-23 3GKR 1 REMARK LINK REVDAT 4 05-SEP-12 3GKR 1 REMARK REVDAT 3 01-AUG-12 3GKR 1 HEADER HET HETATM REMARK REVDAT 3 2 1 SITE REVDAT 2 13-JUL-11 3GKR 1 VERSN REVDAT 1 23-MAR-10 3GKR 0 JRNL AUTH V.DELFOSSE,J.PITON,R.VILLET,M.LECERF,M.ARTHUR,C.MAYER JRNL TITL STRUCTURE OF WEISSELLA VIRIDESCENS FEMX WITH THE JRNL TITL 2 UDP-MURNAC-HEXAPEPTIDE PRODUCT OF THE ALANINE TRANSFER JRNL TITL 3 REACTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 48120 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2533 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3510 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 185 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 514 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.42420 REMARK 3 B22 (A**2) : 0.41960 REMARK 3 B33 (A**2) : 0.43510 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.09430 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.092 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.531 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2833 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3840 ; 2.349 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 334 ; 6.071 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;31.965 ;24.420 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 464 ;13.083 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;22.350 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 405 ; 0.188 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2157 ; 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): 1675 ; 1.466 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2705 ; 2.307 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1158 ; 3.553 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1135 ; 5.217 ; 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 : 1.40 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 3GKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051983. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-06 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 : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97985 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50198 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 27.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : 0.03300 REMARK 200 FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.13900 REMARK 200 R SYM FOR SHELL (I) : 0.13900 REMARK 200 FOR SHELL : 5.600 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: PDB ENTRY 1NE9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG6000, 0.3M CHLORURE DE SODIUM, REMARK 280 0.01M CHLORURE DE MAGNESIUM, 0.07M SULFATE D'AMMONIUM, PH6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 50.91800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 400 REMARK 400 COMPOUND REMARK 400 GROUP: 1 REMARK 400 NAME: UDP-MURNAC-HEXAPEPTIDE PRODUCT REMARK 400 CHAIN: A, B REMARK 400 COMPONENT_1: UDP-MURNAC-PEPTIDE REMARK 400 COMPONENT_2: ALANINE REMARK 400 DESCRIPTION: UDP-MURNAC-HEXAPEPTIDE PRODUCT OF THE ALANINE REMARK 400 TRANSFER REACTION. ALANINE IS TRANSFERRED BY FEMX REMARK 400 TO THE NZ OF LYSINE RESIDUE OF UDP-MURNAC-PEPTIDE 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 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 CG GLU A 16 O HOH A 967 1.97 REMARK 500 O HOH A 739 O HOH A 870 2.08 REMARK 500 O THR A 297 O HOH A 904 2.14 REMARK 500 OE1 GLU A 16 O HOH A 856 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 NE2 GLN A 9 O HOH A 861 1554 2.14 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 145 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 205 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 250 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 LYS B 3 N - CA - CB ANGL. DEV. = -13.7 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 -178.12 171.27 REMARK 500 ASN A 130 -106.73 -152.15 REMARK 500 ASP A 135 -178.95 150.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 64 O REMARK 620 2 THR A 66 O 94.6 REMARK 620 3 HOH A 554 O 86.8 85.8 REMARK 620 4 HOH A 607 O 89.9 174.9 92.0 REMARK 620 5 HOH A 803 O 92.7 92.4 178.1 89.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 280 O REMARK 620 2 ASN A 283 OD1 104.7 REMARK 620 3 HOH A 587 O 86.9 92.1 REMARK 620 4 HOH A 665 O 91.2 163.1 94.6 REMARK 620 5 HOH A 781 O 90.8 83.4 174.3 90.7 REMARK 620 6 HOH A 850 O 176.0 79.1 91.6 85.3 91.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 308 O REMARK 620 2 HOH A 662 O 132.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ALA B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF UDP-MURNAC REMARK 800 -PENTAPEPTIDE 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 DBREF 3GKR A 0 335 UNP Q9EY50 Q9EY50_LACVI 1 336 DBREF 3GKR B 1 5 PDB 3GKR 3GKR 1 5 SEQRES 1 A 336 MET PRO VAL LEU ASN LEU ASN ASP PRO GLN ALA VAL GLU SEQRES 2 A 336 ARG TYR GLU GLU PHE MET ARG GLN SER PRO TYR GLY GLN SEQRES 3 A 336 VAL THR GLN ASP LEU GLY TRP ALA LYS VAL LYS ASN ASN SEQRES 4 A 336 TRP GLU PRO VAL ASP VAL TYR LEU GLU ASP ASP GLN GLY SEQRES 5 A 336 ALA ILE ILE ALA ALA MET SER MET LEU LEU GLY ASP THR SEQRES 6 A 336 PRO THR ASP LYS LYS PHE ALA TYR ALA SER LYS GLY PRO SEQRES 7 A 336 VAL MET ASP VAL THR ASP VAL ASP LEU LEU ASP ARG LEU SEQRES 8 A 336 VAL ASP GLU ALA VAL LYS ALA LEU ASP GLY ARG ALA TYR SEQRES 9 A 336 VAL LEU ARG PHE ASP PRO GLU VAL ALA TYR SER ASP GLU SEQRES 10 A 336 PHE ASN THR THR LEU GLN ASP HIS GLY TYR VAL THR ARG SEQRES 11 A 336 ASN ARG ASN VAL ALA ASP ALA GLY MET HIS ALA THR ILE SEQRES 12 A 336 GLN PRO ARG LEU ASN MET VAL LEU ASP LEU THR LYS PHE SEQRES 13 A 336 PRO ASP ALA LYS THR THR LEU ASP LEU TYR PRO SER LYS SEQRES 14 A 336 THR LYS SER LYS ILE LYS ARG PRO PHE ARG ASP GLY VAL SEQRES 15 A 336 GLU VAL HIS SER GLY ASN SER ALA THR GLU LEU ASP GLU SEQRES 16 A 336 PHE PHE LYS THR TYR THR THR MET ALA GLU ARG HIS GLY SEQRES 17 A 336 ILE THR HIS ARG PRO ILE GLU TYR PHE GLN ARG MET GLN SEQRES 18 A 336 ALA ALA PHE ASP ALA ASP THR MET ARG ILE PHE VAL ALA SEQRES 19 A 336 GLU ARG GLU GLY LYS LEU LEU SER THR GLY ILE ALA LEU SEQRES 20 A 336 LYS TYR GLY ARG LYS ILE TRP TYR MET TYR ALA GLY SER SEQRES 21 A 336 MET ASP GLY ASN THR TYR TYR ALA PRO TYR ALA VAL GLN SEQRES 22 A 336 SER GLU MET ILE GLN TRP ALA LEU ASP THR ASN THR ASP SEQRES 23 A 336 LEU TYR ASP LEU GLY GLY ILE GLU SER GLU SER THR ASP SEQRES 24 A 336 ASP SER LEU TYR VAL PHE LYS HIS VAL PHE VAL LYS ASP SEQRES 25 A 336 ALA PRO ARG GLU TYR ILE GLY GLU ILE ASP LYS VAL LEU SEQRES 26 A 336 ASP PRO GLU VAL TYR ALA GLU LEU VAL LYS ASP SEQRES 1 B 5 UMA FGA LYS DAL DAL MODRES 3GKR UMA B 1 ALA HET UMA B 1 48 HET FGA B 2 9 HET DAL B 4 5 HET DAL B 5 6 HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET GOL A 404 6 HET ALA B 101 5 HETNAM UMA URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE HETNAM FGA GAMMA-D-GLUTAMIC ACID HETNAM DAL D-ALANINE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM ALA ALANINE HETSYN FGA D-GLUTAMIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 UMA C23 H36 N4 O20 P2 FORMUL 2 FGA C5 H9 N O4 FORMUL 2 DAL 2(C3 H7 N O2) FORMUL 3 MG 3(MG 2+) FORMUL 6 GOL C3 H8 O3 FORMUL 7 ALA C3 H7 N O2 FORMUL 8 HOH *514(H2 O) HELIX 1 1 ASP A 7 SER A 21 1 15 HELIX 2 2 GLN A 25 GLN A 28 5 4 HELIX 3 3 ASP A 29 LYS A 36 1 8 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 ASN A 130 ALA A 134 5 5 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 71 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 ILE A 230 N GLY A 186 SHEET 3 B 7 LYS A 238 TYR A 248 -1 O SER A 241 N ALA A 233 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 GLY A 291 1 O ASP A 288 N ILE A 252 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 C22 UMA B 1 N FGA B 2 1555 1555 1.35 LINK CD FGA B 2 N LYS B 3 1555 1555 1.36 LINK C LYS B 3 N DAL B 4 1555 1555 1.33 LINK NZ LYS B 3 C ALA B 101 1555 1555 1.48 LINK C DAL B 4 N DAL B 5 1555 1555 1.31 LINK O THR A 64 MG MG A 401 1555 1555 2.47 LINK O THR A 66 MG MG A 401 1555 1555 2.32 LINK O LEU A 280 MG MG A 402 1555 1555 2.30 LINK OD1 ASN A 283 MG MG A 402 1555 1555 2.39 LINK O PHE A 308 MG MG A 403 1555 1555 2.80 LINK MG MG A 401 O HOH A 554 1555 1555 2.47 LINK MG MG A 401 O HOH A 607 1555 1555 2.40 LINK MG MG A 401 O HOH A 803 1555 1555 2.10 LINK MG MG A 402 O HOH A 587 1555 1555 2.14 LINK MG MG A 402 O HOH A 665 1555 1555 2.37 LINK MG MG A 402 O HOH A 781 1555 1555 2.08 LINK MG MG A 402 O HOH A 850 1555 1555 2.50 LINK MG MG A 403 O HOH A 662 1555 1555 2.68 CISPEP 1 GLY A 76 PRO A 77 0 -3.86 SITE 1 AC1 5 THR A 64 THR A 66 HOH A 554 HOH A 607 SITE 2 AC1 5 HOH A 803 SITE 1 AC2 6 LEU A 280 ASN A 283 HOH A 587 HOH A 665 SITE 2 AC2 6 HOH A 781 HOH A 850 SITE 1 AC3 6 LEU A 150 PHE A 308 VAL A 309 LYS A 310 SITE 2 AC3 6 HOH A 662 HOH A 829 SITE 1 AC4 9 ILE A 54 MET A 79 ASP A 80 LEU A 86 SITE 2 AC4 9 ILE A 213 GLU A 214 HOH A 509 HOH A 533 SITE 3 AC4 9 HOH A 563 SITE 1 AC5 3 UMA B 1 LYS B 3 HOH B 214 SITE 1 AC6 39 TRP A 32 LYS A 36 ASN A 38 TRP A 39 SITE 2 AC6 39 PHE A 70 ASP A 85 TYR A 103 ARG A 106 SITE 3 AC6 39 ILE A 142 ILE A 208 THR A 209 ARG A 211 SITE 4 AC6 39 PRO A 212 TYR A 215 TYR A 256 HOH A 535 SITE 5 AC6 39 HOH A 667 ALA B 101 HOH B 201 HOH B 202 SITE 6 AC6 39 HOH B 203 HOH B 204 HOH B 205 HOH B 206 SITE 7 AC6 39 HOH B 207 HOH B 208 HOH B 209 HOH B 210 SITE 8 AC6 39 HOH B 211 HOH B 212 HOH B 213 HOH B 215 SITE 9 AC6 39 HOH B 216 HOH B 217 HOH B 218 HOH B 220 SITE 10 AC6 39 HOH B 221 HOH B 222 HOH B 223 CRYST1 42.324 101.836 46.847 90.00 102.85 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 0.023627 0.000000 0.005390 0.00000 SCALE2 0.000000 0.009820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021894 0.00000