HEADER LIGASE 21-JAN-05 1VQZ TITLE CRYSTAL STRUCTURE OF A PUTATIVE LIPOATE-PROTEIN LIGASE A (SP_1160) TITLE 2 FROM STREPTOCOCCUS PNEUMONIAE TIGR4 AT 1.99 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOATE-PROTEIN LIGASE, PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 170187; SOURCE 4 STRAIN: TIGR4; SOURCE 5 GENE: NP_345629.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS CLASS II AARS AND BIOTIN SYNTHETASES FOLD, SUFE/NIFU FOLD, STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 25-JAN-23 1VQZ 1 REMARK SEQADV LINK REVDAT 5 04-OCT-17 1VQZ 1 REMARK REVDAT 4 13-JUL-11 1VQZ 1 VERSN REVDAT 3 23-MAR-11 1VQZ 1 HEADER TITLE KEYWDS REVDAT 2 24-FEB-09 1VQZ 1 VERSN REVDAT 1 15-FEB-05 1VQZ 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE LIPOATE-PROTEIN LIGASE JRNL TITL 2 (NP_345629.1) FROM STREPTOCOCCUS PNEUMONIAE TIGR4 AT 1.99 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 24363 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1304 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) : 1.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1704 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2578 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 284 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 31.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.05000 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): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.554 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2704 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2476 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3629 ; 1.530 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5712 ; 0.855 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 6.664 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;32.669 ;24.846 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 446 ;13.039 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;17.708 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 407 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2998 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 552 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 512 ; 0.199 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2529 ; 0.188 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1304 ; 0.175 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1593 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 243 ; 0.151 ; 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): 8 ; 0.193 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 43 ; 0.251 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.198 ; 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): 1706 ; 2.275 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 680 ; 0.584 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2643 ; 3.107 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1152 ; 5.304 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 986 ; 6.743 ;11.000 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 178 REMARK 3 ORIGIN FOR THE GROUP (A): 9.2343 32.9398 15.7997 REMARK 3 T TENSOR REMARK 3 T11: -0.1422 T22: -0.1329 REMARK 3 T33: -0.1098 T12: 0.0227 REMARK 3 T13: 0.0057 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 1.9355 L22: 1.3659 REMARK 3 L33: 1.7203 L12: 0.3212 REMARK 3 L13: 0.6755 L23: -0.1109 REMARK 3 S TENSOR REMARK 3 S11: -0.0004 S12: 0.0106 S13: 0.1958 REMARK 3 S21: 0.1603 S22: 0.0124 S23: 0.1833 REMARK 3 S31: -0.1534 S32: -0.1475 S33: -0.0120 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 179 A 215 REMARK 3 ORIGIN FOR THE GROUP (A): 0.2547 36.8856 4.1396 REMARK 3 T TENSOR REMARK 3 T11: -0.0908 T22: 0.0515 REMARK 3 T33: -0.0413 T12: 0.0469 REMARK 3 T13: -0.0295 T23: 0.0464 REMARK 3 L TENSOR REMARK 3 L11: 4.0885 L22: 1.2907 REMARK 3 L33: 2.7433 L12: 1.3471 REMARK 3 L13: -2.1341 L23: -0.3434 REMARK 3 S TENSOR REMARK 3 S11: 0.0902 S12: 0.2000 S13: 0.4485 REMARK 3 S21: -0.0387 S22: 0.0624 S23: 0.2417 REMARK 3 S31: -0.3919 S32: -0.2802 S33: -0.1526 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 216 A 245 REMARK 3 ORIGIN FOR THE GROUP (A): 23.5959 24.1655 12.6902 REMARK 3 T TENSOR REMARK 3 T11: -0.2041 T22: -0.1369 REMARK 3 T33: -0.0878 T12: 0.0236 REMARK 3 T13: -0.0270 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 1.2752 L22: 3.5031 REMARK 3 L33: 7.5749 L12: 0.0907 REMARK 3 L13: -0.3493 L23: -2.1856 REMARK 3 S TENSOR REMARK 3 S11: -0.0367 S12: 0.1914 S13: -0.1090 REMARK 3 S21: -0.0020 S22: -0.0625 S23: -0.3011 REMARK 3 S31: 0.3148 S32: 0.5788 S33: 0.0992 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 246 A 329 REMARK 3 ORIGIN FOR THE GROUP (A): 22.8008 37.0607 37.5242 REMARK 3 T TENSOR REMARK 3 T11: -0.0437 T22: -0.1795 REMARK 3 T33: -0.1653 T12: -0.0352 REMARK 3 T13: -0.0236 T23: 0.0179 REMARK 3 L TENSOR REMARK 3 L11: 2.5880 L22: 3.0446 REMARK 3 L33: 3.4068 L12: -0.0943 REMARK 3 L13: 1.7273 L23: -0.3702 REMARK 3 S TENSOR REMARK 3 S11: -0.0507 S12: -0.1260 S13: 0.0882 REMARK 3 S21: 0.3481 S22: -0.1342 S23: -0.1514 REMARK 3 S31: -0.1052 S32: 0.1240 S33: 0.1849 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS 2. DISORDERED REGION (RESIDUES OF 172 AND 178) REMARK 3 HAS BEEN MODELED USING XPLEO PROGRAM (H. VAN DEN BEDEM ET AL. REMARK 3 ACTA CRYST. (2005) D61, 2-13) 3. THE ADDITIONAL DENSITY NEAR REMARK 3 GLU170 HAS BEEN MODELED AS AN UNL, UNKNOWN LIGAND, COVALENTLY REMARK 3 BOUND TO THE RESIDUE. REMARK 4 REMARK 4 1VQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000002073. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979724,0.956885,0.979691 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) REMARK 200 OPTICS : FIXED-HEIGHT EXIT BEAM, TOROIDAL REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA 4.2), CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25714 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 29.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13300 REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.71700 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NA2NO3, 20.0% PEG-3350, NO BUFFER REMARK 280 PH 6.8, VAPOR DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 277K 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 22.75150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.81450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.81450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.75150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.14000 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 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 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 MSE A -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 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 0 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 93 CG OD1 ND2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 LYS A 99 CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 GLU A 117 CG CD OE1 OE2 REMARK 470 ARG A 121 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 130 CG CD CE NZ REMARK 470 ASN A 140 CG OD1 ND2 REMARK 470 LYS A 166 CG CD CE NZ REMARK 470 LYS A 168 CG CD CE NZ REMARK 470 LYS A 172 CE NZ REMARK 470 VAL A 174 CG1 CG2 REMARK 470 LYS A 175 CG CD CE NZ REMARK 470 SER A 176 OG REMARK 470 VAL A 177 CG1 CG2 REMARK 470 ARG A 178 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 180 NE CZ NH1 NH2 REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 470 LYS A 207 CD CE NZ REMARK 470 GLU A 219 CD OE1 OE2 REMARK 470 ARG A 227 NE CZ NH1 NH2 REMARK 470 LYS A 242 CG CD CE NZ REMARK 470 GLU A 267 CD OE1 OE2 REMARK 470 LYS A 296 CD CE NZ REMARK 470 GLU A 300 CG CD OE1 OE2 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 142 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -5.0 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 LEU A 25 59.24 -92.98 REMARK 500 ASP A 152 49.62 -156.31 REMARK 500 LYS A 232 -84.31 -127.16 REMARK 500 TYR A 240 -91.62 -109.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 417 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 358040 RELATED DB: TARGETDB DBREF 1VQZ A 1 329 UNP Q97QP1 Q97QP1_STRPN 1 329 SEQADV 1VQZ MSE A -11 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ GLY A -10 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ SER A -9 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ ASP A -8 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ LYS A -7 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ ILE A -6 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ HIS A -5 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ HIS A -4 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ HIS A -3 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ HIS A -2 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ HIS A -1 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ HIS A 0 UNP Q97QP1 EXPRESSION TAG SEQADV 1VQZ MSE A 1 UNP Q97QP1 MET 1 MODIFIED RESIDUE SEQADV 1VQZ MSE A 144 UNP Q97QP1 MET 144 MODIFIED RESIDUE SEQADV 1VQZ MSE A 205 UNP Q97QP1 MET 205 MODIFIED RESIDUE SEQADV 1VQZ MSE A 212 UNP Q97QP1 MET 212 MODIFIED RESIDUE SEQRES 1 A 341 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 341 LYS TYR ILE ILE ASN HIS SER ASN ASP THR ALA PHE ASN SEQRES 3 A 341 ILE ALA LEU GLU GLU TYR ALA PHE LYS HIS LEU LEU ASP SEQRES 4 A 341 GLU ASP GLN ILE PHE LEU LEU TRP ILE ASN LYS PRO SER SEQRES 5 A 341 ILE ILE VAL GLY ARG HIS GLN ASN THR ILE GLU GLU ILE SEQRES 6 A 341 ASN ARG ASP TYR VAL ARG GLU ASN GLY ILE GLU VAL VAL SEQRES 7 A 341 ARG ARG ILE SER GLY GLY GLY ALA VAL TYR HIS ASP LEU SEQRES 8 A 341 ASN ASN LEU ASN TYR THR ILE ILE SER LYS GLU ASP GLU SEQRES 9 A 341 ASN LYS ALA PHE ASP PHE LYS SER PHE SER THR PRO VAL SEQRES 10 A 341 ILE ASN THR LEU ALA GLN LEU GLY VAL LYS ALA GLU PHE SEQRES 11 A 341 THR GLY ARG ASN ASP LEU GLU ILE ASP GLY LYS LYS PHE SEQRES 12 A 341 CYS GLY ASN ALA GLN ALA TYR ILE ASN GLY ARG ILE MSE SEQRES 13 A 341 HIS HIS GLY CYS LEU LEU PHE ASP VAL ASP LEU SER VAL SEQRES 14 A 341 LEU ALA ASN ALA LEU LYS VAL SER LYS ASP LYS PHE GLU SEQRES 15 A 341 SER LYS GLY VAL LYS SER VAL ARG ALA ARG VAL THR ASN SEQRES 16 A 341 ILE ILE ASN GLU LEU PRO LYS LYS ILE THR VAL GLU LYS SEQRES 17 A 341 PHE ARG ASP LEU LEU LEU GLU TYR MSE LYS LYS GLU TYR SEQRES 18 A 341 PRO GLU MSE THR GLU TYR VAL PHE SER GLU GLU GLU LEU SEQRES 19 A 341 ALA GLU ILE ASN ARG ILE LYS ASP THR LYS PHE GLY THR SEQRES 20 A 341 TRP ASP TRP ASN TYR GLY LYS SER PRO GLU PHE ASN VAL SEQRES 21 A 341 ARG ARG GLY ILE LYS PHE THR SER GLY LYS VAL GLU VAL SEQRES 22 A 341 PHE ALA ASN VAL THR GLU SER LYS ILE GLN ASP ILE LYS SEQRES 23 A 341 ILE TYR GLY ASP PHE PHE GLY ILE GLU ASP VAL ALA ALA SEQRES 24 A 341 VAL GLU ASP VAL LEU ARG GLY VAL LYS TYR GLU ARG GLU SEQRES 25 A 341 ASP VAL LEU LYS ALA LEU LYS THR ILE ASP ILE THR ARG SEQRES 26 A 341 TYR PHE ALA GLY ILE SER ARG GLU GLU ILE ALA GLU ALA SEQRES 27 A 341 VAL VAL GLY MODRES 1VQZ MSE A 1 MET SELENOMETHIONINE MODRES 1VQZ MSE A 144 MET SELENOMETHIONINE MODRES 1VQZ MSE A 205 MET SELENOMETHIONINE MODRES 1VQZ MSE A 212 MET SELENOMETHIONINE HET MSE A 1 12 HET MSE A 144 8 HET MSE A 205 8 HET MSE A 212 8 HET UNL A 400 5 HET EDO A 401 4 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 6 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HET EDO A 413 4 HET EDO A 414 4 HET EDO A 415 6 HET EDO A 416 4 HET EDO A 417 4 HETNAM MSE SELENOMETHIONINE HETNAM UNL UNKNOWN LIGAND HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 EDO 17(C2 H6 O2) FORMUL 20 HOH *284(H2 O) HELIX 1 1 ASP A 10 LEU A 25 1 16 HELIX 2 2 ASN A 48 GLU A 52 5 5 HELIX 3 3 ASN A 54 GLY A 62 1 9 HELIX 4 4 ASP A 97 LEU A 112 1 16 HELIX 5 5 SER A 156 LEU A 162 1 7 HELIX 6 6 ASN A 183 GLU A 187 5 5 HELIX 7 7 THR A 193 TYR A 209 1 17 HELIX 8 8 SER A 218 LYS A 232 1 15 HELIX 9 9 THR A 235 TYR A 240 1 6 HELIX 10 10 VAL A 285 ARG A 293 1 9 HELIX 11 11 GLU A 298 LYS A 307 1 10 HELIX 12 12 THR A 308 ILE A 309 5 2 HELIX 13 13 ASP A 310 TYR A 314 5 5 HELIX 14 14 SER A 319 VAL A 328 1 10 SHEET 1 A 8 ALA A 116 THR A 119 0 SHEET 2 A 8 ASP A 123 ILE A 126 -1 O GLU A 125 N GLU A 117 SHEET 3 A 8 LYS A 129 ILE A 139 -1 O LYS A 129 N ILE A 126 SHEET 4 A 8 ARG A 142 LEU A 150 -1 O LEU A 150 N PHE A 131 SHEET 5 A 8 ASN A 81 LYS A 89 -1 N SER A 88 O ILE A 143 SHEET 6 A 8 GLN A 30 TRP A 35 -1 N TRP A 35 O ASN A 83 SHEET 7 A 8 MSE A 1 ILE A 5 1 N LYS A 2 O GLN A 30 SHEET 8 A 8 THR A 213 GLU A 214 1 O THR A 213 N TYR A 3 SHEET 1 B 3 GLU A 64 ARG A 67 0 SHEET 2 B 3 SER A 40 VAL A 43 1 N ILE A 41 O GLU A 64 SHEET 3 B 3 VAL A 75 HIS A 77 -1 O VAL A 75 N ILE A 42 SHEET 1 C 4 GLU A 170 SER A 171 0 SHEET 2 C 4 VAL A 248 PHE A 254 1 O LYS A 253 N GLU A 170 SHEET 3 C 4 GLY A 257 THR A 266 -1 O VAL A 259 N ILE A 252 SHEET 4 C 4 LYS A 269 GLY A 277 -1 O LYS A 274 N PHE A 262 LINK C HIS A 0 N MSE A 1 1555 1555 1.35 LINK C MSE A 1 N LYS A 2 1555 1555 1.32 LINK C ILE A 143 N MSE A 144 1555 1555 1.34 LINK C MSE A 144 N HIS A 145 1555 1555 1.32 LINK OE1 GLU A 170 C2 UNL A 400 1555 1555 1.60 LINK C TYR A 204 N MSE A 205 1555 1555 1.34 LINK C MSE A 205 N LYS A 206 1555 1555 1.34 LINK C BGLU A 211 N MSE A 212 1555 1555 1.33 LINK C AGLU A 211 N MSE A 212 1555 1555 1.33 LINK C MSE A 212 N THR A 213 1555 1555 1.33 SITE 1 AC1 6 TYR A 3 GLU A 170 LYS A 206 ARG A 250 SITE 2 AC1 6 GLY A 251 HOH A 612 SITE 1 AC2 3 ASN A 54 ARG A 55 ASP A 56 SITE 1 AC3 8 ARG A 45 HIS A 46 LYS A 274 ILE A 275 SITE 2 AC3 8 TYR A 276 EDO A 407 EDO A 417 HOH A 490 SITE 1 AC4 5 ASP A 199 LEU A 202 GLU A 203 GLY A 329 SITE 2 AC4 5 HOH A 578 SITE 1 AC5 9 LYS A 23 HIS A 24 ASN A 186 GLU A 187 SITE 2 AC5 9 PRO A 189 EDO A 416 HOH A 519 HOH A 649 SITE 3 AC5 9 HOH A 662 SITE 1 AC6 5 THR A 235 TRP A 236 ASP A 237 LYS A 307 SITE 2 AC6 5 ARG A 320 SITE 1 AC7 3 LYS A 232 EDO A 412 HOH A 596 SITE 1 AC8 6 ASP A 237 TRP A 238 TYR A 240 EDO A 402 SITE 2 AC8 6 EDO A 417 HOH A 602 SITE 1 AC9 6 ASN A 48 ILE A 50 SER A 243 PHE A 262 SITE 2 AC9 6 TYR A 276 HOH A 536 SITE 1 BC1 7 ARG A 68 VAL A 75 GLY A 147 EDO A 410 SITE 2 BC1 7 HOH A 441 HOH A 450 HOH A 624 SITE 1 BC2 7 GLU A 18 HIS A 77 HIS A 146 EDO A 409 SITE 2 BC2 7 HOH A 426 HOH A 441 HOH A 450 SITE 1 BC3 5 HIS A 7 ASN A 9 ILE A 36 ARG A 198 SITE 2 BC3 5 HOH A 676 SITE 1 BC4 8 GLU A 19 LYS A 23 HIS A 24 ILE A 228 SITE 2 BC4 8 LYS A 232 EDO A 406 HOH A 649 HOH A 650 SITE 1 BC5 5 LYS A 196 ASP A 199 GLU A 203 GLY A 329 SITE 2 BC5 5 HOH A 655 SITE 1 BC6 5 ASN A 122 ASN A 134 ALA A 135 GLN A 136 SITE 2 BC6 5 PHE A 280 SITE 1 BC7 6 ILE A 50 ARG A 55 TYR A 240 HOH A 517 SITE 2 BC7 6 HOH A 547 HOH A 700 SITE 1 BC8 3 LYS A 129 GLU A 187 EDO A 404 SITE 1 BC9 8 ARG A 45 HIS A 46 ASP A 284 EDO A 402 SITE 2 BC9 8 EDO A 407 HOH A 467 HOH A 490 HOH A 673 CRYST1 45.503 70.280 113.629 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 0.021977 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014229 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008801 0.00000