HEADER TRANSFERASE 20-AUG-04 1VLY TITLE CRYSTAL STRUCTURE OF A PUTATIVE AMINOMETHYLTRANSFERASE (YGFZ) FROM TITLE 2 ESCHERICHIA COLI AT 1.30 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNKNOWN PROTEIN FROM 2D-PAGE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SPOT PR51; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: YGFZ, B2898; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 25-JAN-23 1VLY 1 REMARK SEQADV LINK REVDAT 5 23-MAR-11 1VLY 1 HEADER TITLE KEYWDS REVDAT 4 24-FEB-09 1VLY 1 VERSN REVDAT 3 28-MAR-06 1VLY 1 JRNL REVDAT 2 18-JAN-05 1VLY 1 AUTHOR KEYWDS REMARK REVDAT 1 31-AUG-04 1VLY 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF UNKNOWN PROTEIN FROM 2D-PAGE (SPOT JRNL TITL 2 PR51) (B2898) FROM ESCHERICHIA COLI K12 AT 1.30 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 71946 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) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3802 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3189 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 53.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 170 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2475 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 477 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.68000 REMARK 3 B12 (A**2) : 0.37000 REMARK 3 B13 (A**2) : -0.09000 REMARK 3 B23 (A**2) : 0.28000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.048 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.047 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.364 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2588 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2397 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3510 ; 1.495 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5569 ; 1.052 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 324 ; 6.461 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;34.927 ;24.696 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 442 ;11.940 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;12.108 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 402 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2871 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 502 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 462 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2425 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1261 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1610 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 377 ; 0.150 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.107 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 5 ; 0.378 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 40 ; 0.263 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 35 ; 0.201 ; 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): 1682 ; 2.427 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 656 ; 1.411 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2613 ; 3.171 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1043 ; 4.135 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 897 ; 5.375 ;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): 5490 ; 1.938 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 479 ; 6.506 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4938 ; 3.452 ; 3.000 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. 1. TWO CALCIUM CATIONS WERE TENTAIVELY MODELED INTO REMARK 3 THE STRUCTURE BASED ON THE INCLUSION OF 0.2M CALCIUM ACETATE IN REMARK 3 THE CRYSTALLIZATION, AND PROXIMITY OF THE TWO SITES TO REMARK 3 NEGATIVELY-CHARGED AMINO ACID SIDECHAINS. THE BOND VALENCE REMARK 3 (MULLER ET AL. ACTA CRYST D. 2003 D59 PP. 32-37) ALSO INDICATES REMARK 3 ASSIGNING A CA+2 CATION AT THIS POSITION. 2. THE ELECTRON REMARK 3 DENSITY BETWEEN RESIDUES A260-A264 AND A269-A272 IS WEAK, REMARK 3 THEREFORE, IT WAS NOT POSSIBLE TO BUILD SIDECHAIN COORDINATES IN REMARK 3 THIS REGION. REMARK 4 REMARK 4 1VLY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000001995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-04; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRL; SSRL REMARK 200 BEAMLINE : BL11-1; BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979129; 0.979508,0.885567 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(311) BENT REMARK 200 MONOCHROMATOR; NULL REMARK 200 OPTICS : FLAT MIRROR; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 4.2), CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75749 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 26.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03600 REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33900 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; 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 (%): 41.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M CAACETATE, 20.0% PEG-3350, NO REMARK 280 BUFFER PH 7.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 465 HIS A 0 REMARK 465 MSE A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 326 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 66 CD CE NZ REMARK 470 GLU A 92 CD OE1 OE2 REMARK 470 LYS A 100 CD CE NZ REMARK 470 GLU A 114 CG CD OE1 OE2 REMARK 470 GLU A 233 CD OE1 OE2 REMARK 470 ARG A 237 CZ NH1 NH2 REMARK 470 ARG A 241 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 245 CD CE NZ REMARK 470 GLU A 271 CG CD OE1 OE2 REMARK 470 ARG A 274 CD NE CZ NH1 NH2 REMARK 470 GLU A 325 CG CD OE1 OE2 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 663 O HOH A 696 2.10 REMARK 500 O HOH A 771 O HOH A 971 2.12 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 O2 EDO A 503 O HOH A 733 1655 2.04 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 MSE A 52 SE MSE A 52 CE -0.382 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 MSE A 52 CB - CG - SE ANGL. DEV. = -18.1 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 THR A 4 128.17 91.62 REMARK 500 LEU A 24 54.44 -102.98 REMARK 500 GLU A 180 -53.74 -120.34 REMARK 500 ASN A 185 -159.92 -110.37 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 CA A 505 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 286 OE1 REMARK 620 2 GLU A 286 OE2 51.4 REMARK 620 3 HOH A 585 O 146.3 159.8 REMARK 620 4 HOH A 587 O 74.1 123.8 76.3 REMARK 620 5 HOH A 655 O 79.9 76.9 111.2 81.4 REMARK 620 6 HOH A 752 O 85.0 94.1 81.4 94.0 164.9 REMARK 620 7 HOH A 832 O 114.3 70.2 89.8 160.9 116.3 70.6 REMARK 620 8 HOH A 875 O 135.4 90.0 76.6 128.3 68.7 124.1 58.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 358289 RELATED DB: TARGETDB DBREF 1VLY A 2 326 UNP P39179 UP14_ECOLI 1 325 SEQADV 1VLY MSE A -11 UNP P39179 EXPRESSION TAG SEQADV 1VLY GLY A -10 UNP P39179 EXPRESSION TAG SEQADV 1VLY SER A -9 UNP P39179 EXPRESSION TAG SEQADV 1VLY ASP A -8 UNP P39179 EXPRESSION TAG SEQADV 1VLY LYS A -7 UNP P39179 EXPRESSION TAG SEQADV 1VLY ILE A -6 UNP P39179 EXPRESSION TAG SEQADV 1VLY HIS A -5 UNP P39179 EXPRESSION TAG SEQADV 1VLY HIS A -4 UNP P39179 EXPRESSION TAG SEQADV 1VLY HIS A -3 UNP P39179 EXPRESSION TAG SEQADV 1VLY HIS A -2 UNP P39179 EXPRESSION TAG SEQADV 1VLY HIS A -1 UNP P39179 EXPRESSION TAG SEQADV 1VLY HIS A 0 UNP P39179 EXPRESSION TAG SEQADV 1VLY MSE A 1 UNP P39179 EXPRESSION TAG SEQADV 1VLY MSE A 22 UNP P39179 MET 21 MODIFIED RESIDUE SEQADV 1VLY MSE A 41 UNP P39179 MET 40 MODIFIED RESIDUE SEQADV 1VLY MSE A 52 UNP P39179 MET 51 MODIFIED RESIDUE SEQADV 1VLY MSE A 69 UNP P39179 MET 68 MODIFIED RESIDUE SEQADV 1VLY MSE A 172 UNP P39179 MET 171 MODIFIED RESIDUE SEQADV 1VLY MSE A 234 UNP P39179 MET 233 MODIFIED RESIDUE SEQADV 1VLY MSE A 269 UNP P39179 MET 268 MODIFIED RESIDUE SEQADV 1VLY MSE A 296 UNP P39179 MET 295 MODIFIED RESIDUE SEQADV 1VLY MSE A 300 UNP P39179 MET 299 MODIFIED RESIDUE SEQRES 1 A 338 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MSE SEQRES 2 A 338 ALA PHE THR PRO PHE PRO PRO ARG GLN PRO THR ALA SER SEQRES 3 A 338 ALA ARG LEU PRO LEU THR LEU MSE THR LEU ASP ASP TRP SEQRES 4 A 338 ALA LEU ALA THR ILE THR GLY ALA ASP SER GLU LYS TYR SEQRES 5 A 338 MSE GLN GLY GLN VAL THR ALA ASP VAL SER GLN MSE ALA SEQRES 6 A 338 GLU ASP GLN HIS LEU LEU ALA ALA HIS CYS ASP ALA LYS SEQRES 7 A 338 GLY LYS MSE TRP SER ASN LEU ARG LEU PHE ARG ASP GLY SEQRES 8 A 338 ASP GLY PHE ALA TRP ILE GLU ARG ARG SER VAL ARG GLU SEQRES 9 A 338 PRO GLN LEU THR GLU LEU LYS LYS TYR ALA VAL PHE SER SEQRES 10 A 338 LYS VAL THR ILE ALA PRO ASP ASP GLU ARG VAL LEU LEU SEQRES 11 A 338 GLY VAL ALA GLY PHE GLN ALA ARG ALA ALA LEU ALA ASN SEQRES 12 A 338 LEU PHE SER GLU LEU PRO SER LYS GLU LYS GLN VAL VAL SEQRES 13 A 338 LYS GLU GLY ALA THR THR LEU LEU TRP PHE GLU HIS PRO SEQRES 14 A 338 ALA GLU ARG PHE LEU ILE VAL THR ASP GLU ALA THR ALA SEQRES 15 A 338 ASN MSE LEU THR ASP LYS LEU ARG GLY GLU ALA GLU LEU SEQRES 16 A 338 ASN ASN SER GLN GLN TRP LEU ALA LEU ASN ILE GLU ALA SEQRES 17 A 338 GLY PHE PRO VAL ILE ASP ALA ALA ASN SER GLY GLN PHE SEQRES 18 A 338 ILE PRO GLN ALA THR ASN LEU GLN ALA LEU GLY GLY ILE SEQRES 19 A 338 SER PHE LYS LYS GLY CYS TYR THR GLY GLN GLU MSE VAL SEQRES 20 A 338 ALA ARG ALA LYS PHE ARG GLY ALA ASN LYS ARG ALA LEU SEQRES 21 A 338 TRP LEU LEU ALA GLY SER ALA SER ARG LEU PRO GLU ALA SEQRES 22 A 338 GLY GLU ASP LEU GLU LEU LYS MSE GLY GLU ASN TRP ARG SEQRES 23 A 338 ARG THR GLY THR VAL LEU ALA ALA VAL LYS LEU GLU ASP SEQRES 24 A 338 GLY GLN VAL VAL VAL GLN VAL VAL MSE ASN ASN ASP MSE SEQRES 25 A 338 GLU PRO ASP SER ILE PHE ARG VAL ARG ASP ASP ALA ASN SEQRES 26 A 338 THR LEU HIS ILE GLU PRO LEU PRO TYR SER LEU GLU GLU MODRES 1VLY MSE A 22 MET SELENOMETHIONINE MODRES 1VLY MSE A 41 MET SELENOMETHIONINE MODRES 1VLY MSE A 52 MET SELENOMETHIONINE MODRES 1VLY MSE A 69 MET SELENOMETHIONINE MODRES 1VLY MSE A 172 MET SELENOMETHIONINE MODRES 1VLY MSE A 234 MET SELENOMETHIONINE MODRES 1VLY MSE A 269 MET SELENOMETHIONINE MODRES 1VLY MSE A 296 MET SELENOMETHIONINE MODRES 1VLY MSE A 300 MET SELENOMETHIONINE HET MSE A 22 8 HET MSE A 41 8 HET MSE A 52 10 HET MSE A 69 8 HET MSE A 172 8 HET MSE A 234 8 HET MSE A 269 8 HET MSE A 296 8 HET MSE A 300 12 HET ACT A 504 4 HET CA A 505 1 HET CL A 506 1 HET EDO A 501 4 HET EDO A 502 4 HET EDO A 503 5 HETNAM MSE SELENOMETHIONINE HETNAM ACT ACETATE ION HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 CA CA 2+ FORMUL 4 CL CL 1- FORMUL 5 EDO 3(C2 H6 O2) FORMUL 8 HOH *477(H2 O) HELIX 1 1 ALA A 13 LEU A 17 5 5 HELIX 2 2 ASP A 36 GLY A 43 1 8 HELIX 3 3 ASP A 48 MSE A 52 5 5 HELIX 4 4 ARG A 88 LYS A 100 1 13 HELIX 5 5 GLN A 124 ASN A 131 1 8 HELIX 6 6 ASP A 166 ARG A 178 1 13 HELIX 7 7 ASN A 185 GLY A 197 1 13 HELIX 8 8 ASP A 202 SER A 206 5 5 HELIX 9 9 ILE A 210 LEU A 219 5 10 HELIX 10 10 GLY A 231 ALA A 238 1 8 SHEET 1 A 6 VAL A 143 GLU A 146 0 SHEET 2 A 6 THR A 149 PHE A 154 -1 O LEU A 151 N VAL A 144 SHEET 3 A 6 ARG A 160 THR A 165 -1 O LEU A 162 N LEU A 152 SHEET 4 A 6 VAL A 116 ALA A 121 -1 N VAL A 116 O THR A 165 SHEET 5 A 6 THR A 20 THR A 23 -1 N THR A 20 O ALA A 121 SHEET 6 A 6 GLU A 182 ASN A 184 1 O GLU A 182 N LEU A 21 SHEET 1 B 5 HIS A 57 CYS A 63 0 SHEET 2 B 5 MSE A 69 ASP A 78 -1 O LEU A 75 N LEU A 58 SHEET 3 B 5 GLY A 81 ARG A 87 -1 O ALA A 83 N PHE A 76 SHEET 4 B 5 TRP A 27 THR A 33 -1 N ALA A 28 O GLU A 86 SHEET 5 B 5 THR A 108 ASP A 112 -1 O ALA A 110 N THR A 31 SHEET 1 C 4 THR A 278 LYS A 284 0 SHEET 2 C 4 VAL A 290 ASN A 297 -1 O GLN A 293 N LEU A 280 SHEET 3 C 4 ARG A 246 GLY A 253 -1 N TRP A 249 O VAL A 294 SHEET 4 C 4 LEU A 315 GLU A 318 -1 O GLU A 318 N LEU A 250 SHEET 1 D 3 ASN A 272 THR A 276 0 SHEET 2 D 3 LEU A 265 MSE A 269 -1 N LEU A 265 O THR A 276 SHEET 3 D 3 PHE A 306 ARG A 307 -1 O ARG A 307 N GLU A 266 LINK C LEU A 21 N MSE A 22 1555 1555 1.33 LINK C MSE A 22 N THR A 23 1555 1555 1.33 LINK C TYR A 40 N MSE A 41 1555 1555 1.33 LINK C MSE A 41 N GLN A 42 1555 1555 1.33 LINK C GLN A 51 N MSE A 52 1555 1555 1.32 LINK C MSE A 52 N ALA A 53 1555 1555 1.33 LINK C LYS A 68 N MSE A 69 1555 1555 1.34 LINK C MSE A 69 N TRP A 70 1555 1555 1.32 LINK C ASN A 171 N MSE A 172 1555 1555 1.34 LINK C MSE A 172 N LEU A 173 1555 1555 1.33 LINK C GLU A 233 N MSE A 234 1555 1555 1.33 LINK C MSE A 234 N VAL A 235 1555 1555 1.33 LINK C LYS A 268 N MSE A 269 1555 1555 1.32 LINK C MSE A 269 N GLY A 270 1555 1555 1.33 LINK C VAL A 295 N MSE A 296 1555 1555 1.32 LINK C MSE A 296 N ASN A 297 1555 1555 1.32 LINK C ASP A 299 N MSE A 300 1555 1555 1.33 LINK C MSE A 300 N GLU A 301 1555 1555 1.33 LINK OE1 GLU A 286 CA CA A 505 1555 1555 2.57 LINK OE2 GLU A 286 CA CA A 505 1555 1555 2.50 LINK CA CA A 505 O HOH A 585 1555 1555 2.35 LINK CA CA A 505 O HOH A 587 1555 1555 2.37 LINK CA CA A 505 O HOH A 655 1555 1555 2.29 LINK CA CA A 505 O HOH A 752 1555 1555 2.37 LINK CA CA A 505 O HOH A 832 1555 1555 2.25 LINK CA CA A 505 O HOH A 875 1555 1555 2.59 CISPEP 1 HIS A 156 PRO A 157 0 -1.72 SITE 1 AC1 7 TRP A 27 ARG A 74 LEU A 162 TRP A 189 SITE 2 AC1 7 ASN A 193 HOH A 527 HOH A 558 SITE 1 AC2 7 GLU A 286 HOH A 585 HOH A 587 HOH A 655 SITE 2 AC2 7 HOH A 752 HOH A 832 HOH A 875 SITE 1 AC3 5 LYS A 68 PHE A 209 ILE A 210 ARG A 246 SITE 2 AC3 5 HOH A 827 SITE 1 AC4 7 THR A 23 LEU A 24 ASP A 25 VAL A 116 SITE 2 AC4 7 LEU A 117 HOH A 568 HOH A 661 SITE 1 AC5 7 ARG A 16 LYS A 99 VAL A 107 THR A 108 SITE 2 AC5 7 ILE A 109 HOH A 633 HOH A 797 SITE 1 AC6 4 GLU A 38 SER A 50 GLU A 260 HOH A 733 CRYST1 44.814 50.080 52.014 94.68 115.29 116.46 P 1 1 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 0.022314 0.011106 0.015155 0.00000 SCALE2 0.000000 0.022305 0.007956 0.00000 SCALE3 0.000000 0.000000 0.022576 0.00000