HEADER HYDROLASE 04-FEB-14 4OX5 TITLE STRUCTURE OF THE LDCB LD-CARBOXYPEPTIDASE REVEALS THE MOLECULAR BASIS TITLE 2 OF PEPTIDOGLYCAN RECOGNITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LDCB LD-CARBOXYPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 56-238; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 171101; SOURCE 4 STRAIN: R6; SOURCE 5 GENE: SPR0554; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS LAS FAMILY, LD-CARBOXYPEPTIDASE, CELL WALL MODIFYING ENZYME, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.N.HOYLAND,C.ALDRIDGE,R.M.CLEVERLEY,K.SIDIQ,M.C.DUCHENE,R.A.DANIEL, AUTHOR 2 W.VOLLMER,R.J.LEWIS REVDAT 6 27-DEC-23 4OX5 1 REMARK LINK REVDAT 5 01-JAN-20 4OX5 1 REMARK REVDAT 4 27-SEP-17 4OX5 1 SOURCE KEYWDS JRNL REMARK REVDAT 3 01-OCT-14 4OX5 1 JRNL REVDAT 2 16-JUL-14 4OX5 1 JRNL REVDAT 1 21-MAY-14 4OX5 0 JRNL AUTH C.N.HOYLAND,C.ALDRIDGE,R.M.CLEVERLEY,M.C.DUCHENE,G.MINASOV, JRNL AUTH 2 O.ONOPRIYENKO,K.SIDIQ,P.J.STOGIOS,W.F.ANDERSON,R.A.DANIEL, JRNL AUTH 3 A.SAVCHENKO,W.VOLLMER,R.J.LEWIS JRNL TITL STRUCTURE OF THE LDCB LD-CARBOXYPEPTIDASE REVEALS THE JRNL TITL 2 MOLECULAR BASIS OF PEPTIDOGLYCAN RECOGNITION. JRNL REF STRUCTURE V. 22 949 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 24909784 JRNL DOI 10.1016/J.STR.2014.04.015 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 18174 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 955 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1157 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1468 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 198 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.75000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : -2.73000 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): 0.136 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.944 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1538 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1382 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2063 ; 2.003 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3186 ; 0.839 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 183 ; 6.460 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;31.336 ;24.810 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 237 ;13.999 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;13.804 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 207 ; 0.249 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1744 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 353 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 742 ; 3.731 ; 3.947 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 740 ; 3.712 ; 3.945 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 921 ; 4.764 ; 5.891 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 922 ; 4.762 ; 5.894 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 796 ; 4.626 ; 4.365 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 797 ; 4.623 ; 4.371 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1143 ; 6.053 ; 6.422 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2020 ;12.198 ;34.574 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2021 ;12.196 ;34.599 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 4OX5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000200172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25656 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 24.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : 14.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MIXTURE OF AMINO ACIDS (GLYCINE, REMARK 280 L-GLUTAMATE, AND RACEMATES OF ALANINE, SERINE AND LYSINE), 0.1 M REMARK 280 BUFFER SYSTEM 2, PH 7.5 AND 37.5 % MPD/PEG1000/PEG3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.42750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.20700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 69.13450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.42750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.20700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.13450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.42750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.20700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.13450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.42750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 30.20700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 69.13450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -477.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 48.85500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 60.41400 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 48.85500 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 138.26900 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 60.41400 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 138.26900 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 A 403 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 425 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 468 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 GLN A 135 REMARK 465 ASP A 136 REMARK 465 ASP A 238 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 LYS A 138 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MSE A 202 SE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 561 O HOH A 588 1.85 REMARK 500 O HOH A 580 O HOH A 590 2.03 REMARK 500 O HOH A 539 O HOH A 554 2.07 REMARK 500 O HOH A 455 O HOH A 516 2.12 REMARK 500 O SER A -3 O HOH A 565 2.17 REMARK 500 O GLY A -4 O HOH A 530 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 460 O HOH A 461 8455 1.77 REMARK 500 O HOH A 401 O HOH A 445 3656 1.91 REMARK 500 O HOH A 444 O HOH A 444 3656 2.09 REMARK 500 O HOH A 427 O HOH A 452 3656 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 196 CD GLU A 196 OE2 0.078 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 A 160 OD1 - CG - OD2 ANGL. DEV. = 15.6 DEGREES REMARK 500 ASP A 160 CB - CG - OD2 ANGL. DEV. = -12.1 DEGREES REMARK 500 MSE A 202 CG - SE - CE ANGL. DEV. = -14.1 DEGREES REMARK 500 ASP A 235 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES 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 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A -2 NE2 REMARK 620 2 GLU A 56 OE1 83.5 REMARK 620 3 GLU A 56 OE2 112.9 57.2 REMARK 620 4 HIS A 79 NE2 132.8 127.6 72.5 REMARK 620 5 HOH A 408 O 145.0 123.5 73.4 13.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 115 NE2 REMARK 620 2 HIS A 181 ND1 59.4 REMARK 620 3 ASP A 184 OD2 58.0 7.6 REMARK 620 4 TRS A 305 N 56.5 5.0 3.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 153 NE2 REMARK 620 2 ASP A 160 OD1 112.1 REMARK 620 3 ASP A 160 OD2 83.2 57.7 REMARK 620 4 HIS A 207 ND1 103.2 98.7 155.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DAL A 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OX3 RELATED DB: PDB REMARK 900 RELATED ID: 4OXD RELATED DB: PDB DBREF 4OX5 A 56 238 UNP Q8DQQ1 Q8DQQ1_STRR6 56 238 SEQADV 4OX5 GLY A -4 UNP Q8DQQ1 EXPRESSION TAG SEQADV 4OX5 SER A -3 UNP Q8DQQ1 EXPRESSION TAG SEQADV 4OX5 HIS A -2 UNP Q8DQQ1 EXPRESSION TAG SEQADV 4OX5 MSE A -1 UNP Q8DQQ1 EXPRESSION TAG SEQRES 1 A 187 GLY SER HIS MSE GLU VAL VAL ASN LYS GLY ASP TYR TYR SEQRES 2 A 187 SER ILE GLN GLY LYS TYR ASP GLU ILE ILE VAL ALA ASN SEQRES 3 A 187 LYS HIS TYR PRO LEU SER LYS ASP TYR ASN PRO GLY GLU SEQRES 4 A 187 ASN PRO THR ALA LYS ALA GLU LEU VAL LYS LEU ILE LYS SEQRES 5 A 187 ALA MSE GLN GLU ALA GLY PHE PRO ILE SER ASP HIS TYR SEQRES 6 A 187 SER GLY PHE ARG SER TYR GLU THR GLN THR LYS LEU TYR SEQRES 7 A 187 GLN ASP TYR VAL ASN GLN ASP GLY LYS GLU ALA ALA ASP SEQRES 8 A 187 ARG TYR SER ALA ARG PRO GLY TYR SER GLU HIS GLN THR SEQRES 9 A 187 GLY LEU ALA PHE ASP VAL ILE GLY THR ASP GLY ASP LEU SEQRES 10 A 187 VAL THR GLU GLU LYS ALA ALA GLN TRP LEU LEU ASP HIS SEQRES 11 A 187 ALA ALA ASP TYR GLY PHE VAL VAL ARG TYR LEU LYS GLY SEQRES 12 A 187 LYS GLU LYS GLU THR GLY TYR MSE ALA GLU GLU TRP HIS SEQRES 13 A 187 LEU ARG TYR VAL GLY LYS GLU ALA LYS GLU ILE ALA GLU SEQRES 14 A 187 SER GLY LEU SER LEU GLU GLU TYR TYR GLY PHE GLU GLY SEQRES 15 A 187 GLY ASP TYR VAL ASP MODRES 4OX5 MSE A 105 MET MODIFIED RESIDUE MODRES 4OX5 MSE A 202 MET MODIFIED RESIDUE HET MSE A -1 8 HET MSE A 105 8 HET MSE A 202 16 HET ZN A 301 1 HET ZN A 302 1 HET ZN A 303 1 HET CL A 304 1 HET TRS A 305 8 HET MPD A 306 8 HET DAL A 307 6 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM DAL D-ALANINE HETSYN TRS TRIS BUFFER FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 ZN 3(ZN 2+) FORMUL 5 CL CL 1- FORMUL 6 TRS C4 H12 N O3 1+ FORMUL 7 MPD C6 H14 O2 FORMUL 8 DAL C3 H7 N O2 FORMUL 9 HOH *198(H2 O) HELIX 1 AA1 ASN A 91 ALA A 108 1 18 HELIX 2 AA2 SER A 121 ASN A 134 1 14 HELIX 3 AA3 LYS A 138 SER A 145 1 8 HELIX 4 AA4 SER A 151 GLY A 156 5 6 HELIX 5 AA5 GLU A 171 ALA A 182 1 12 HELIX 6 AA6 ALA A 183 TYR A 185 5 3 HELIX 7 AA7 LYS A 195 GLY A 200 1 6 HELIX 8 AA8 GLU A 214 GLY A 222 1 9 HELIX 9 AA9 SER A 224 GLY A 230 1 7 SHEET 1 AA1 3 VAL A 58 ASN A 59 0 SHEET 2 AA1 3 TYR A 64 GLN A 67 -1 O SER A 65 N VAL A 58 SHEET 3 AA1 3 GLU A 72 VAL A 75 -1 O ILE A 73 N ILE A 66 SHEET 1 AA2 4 ILE A 112 SER A 117 0 SHEET 2 AA2 4 ALA A 158 GLY A 163 -1 O ILE A 162 N SER A 113 SHEET 3 AA2 4 HIS A 207 TYR A 210 -1 O LEU A 208 N PHE A 159 SHEET 4 AA2 4 PHE A 187 VAL A 189 -1 N VAL A 188 O ARG A 209 LINK C HIS A -2 N MSE A -1 1555 1555 1.32 LINK C MSE A -1 N GLU A 56 1555 1555 1.46 LINK C ALA A 104 N MSE A 105 1555 1555 1.34 LINK C MSE A 105 N GLN A 106 1555 1555 1.33 LINK C TYR A 201 N AMSE A 202 1555 1555 1.33 LINK C TYR A 201 N BMSE A 202 1555 1555 1.33 LINK C AMSE A 202 N ALA A 203 1555 1555 1.34 LINK C BMSE A 202 N ALA A 203 1555 1555 1.32 LINK NE2 HIS A -2 ZN ZN A 303 1555 3656 2.13 LINK OE1 GLU A 56 ZN ZN A 303 1555 3656 2.53 LINK OE2 GLU A 56 ZN ZN A 303 1555 3656 2.04 LINK NE2 HIS A 79 ZN ZN A 303 1555 1555 2.11 LINK NE2 HIS A 115 ZN ZN A 301 1555 8555 2.26 LINK NE2 HIS A 153 ZN ZN A 302 1555 1555 2.10 LINK OD1 ASP A 160 ZN ZN A 302 1555 1555 1.93 LINK OD2 ASP A 160 ZN ZN A 302 1555 1555 2.62 LINK ND1 HIS A 181 ZN ZN A 301 1555 1555 2.15 LINK OD2 ASP A 184 ZN ZN A 301 1555 1555 2.09 LINK ND1 HIS A 207 ZN ZN A 302 1555 1555 2.14 LINK ZN ZN A 301 N TRS A 305 1555 8455 1.96 LINK ZN ZN A 303 O HOH A 408 1555 1555 1.87 CISPEP 1 SER A -3 HIS A -2 0 -23.98 SITE 1 AC1 4 HIS A 115 HIS A 181 ASP A 184 TRS A 305 SITE 1 AC2 3 HIS A 153 ASP A 160 HIS A 207 SITE 1 AC3 4 HIS A -2 GLU A 56 HIS A 79 HOH A 408 SITE 1 AC4 8 ASP A 114 HIS A 115 GLU A 172 ASP A 180 SITE 2 AC4 8 HIS A 181 ASP A 184 ZN A 301 HOH A 426 SITE 1 AC5 4 THR A 170 GLU A 171 HOH A 523 HOH A 563 SITE 1 AC6 8 TYR A 144 ALA A 146 SER A 151 HIS A 153 SITE 2 AC6 8 TYR A 201 GLU A 204 HOH A 486 HOH A 591 CRYST1 48.855 60.414 138.269 90.00 90.00 90.00 I 2 2 2 8 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 0.020469 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007232 0.00000