HEADER SIGNALING PROTEIN 01-APR-10 3MF4 TITLE CRYSTAL STRUCTURE OF PUTATIVE TWO-COMPONENT SYSTEM RESPONSE TITLE 2 REGULATOR/GGDEF DOMAIN PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TWO-COMPONENT SYSTEM RESPONSE REGULATOR/GGDEF DOMAIN COMPND 3 PROTEIN; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: SEQUENCE DATABASE RESIDUES 2-249; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROMONAS SALMONICIDA; SOURCE 3 ORGANISM_TAXID: 382245; SOURCE 4 STRAIN: A449; SOURCE 5 GENE: ASA_2441; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODON+RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: BC-PSGX3(BC) KEYWDS STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, NYSGXRC, TWO- KEYWDS 2 COMPONENT SYSTEM RESPONSE REGULATOR, PSI-2, NEW YORK SGX RESEARCH KEYWDS 3 CENTER FOR STRUCTURAL GENOMICS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.N.MALASHKEVICH,R.TORO,J.M.SAUDER,S.K.BURLEY,S.C.ALMO,NEW YORK SGX AUTHOR 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 9 06-NOV-24 3MF4 1 REMARK REVDAT 8 22-NOV-23 3MF4 1 REMARK REVDAT 7 06-SEP-23 3MF4 1 REMARK REVDAT 6 06-OCT-21 3MF4 1 SEQADV REVDAT 5 10-FEB-21 3MF4 1 AUTHOR JRNL REMARK SEQADV REVDAT 5 2 1 LINK REVDAT 4 21-NOV-18 3MF4 1 AUTHOR REVDAT 3 08-NOV-17 3MF4 1 REMARK REVDAT 2 13-JUL-11 3MF4 1 VERSN REVDAT 1 14-APR-10 3MF4 0 JRNL AUTH V.N.MALASHKEVICH,R.TORO,J.M.SAUDER,S.K.BURLEY,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE TWO-COMPONENT SYSTEM RESPONSE JRNL TITL 2 REGULATOR/GGDEF DOMAIN PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.1 REMARK 3 NUMBER OF REFLECTIONS : 33220 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1662 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) : 1229 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 44.46 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3898 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : -0.20000 REMARK 3 B13 (A**2) : 0.03000 REMARK 3 B23 (A**2) : -0.34000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.230 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.181 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4033 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5466 ; 1.285 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 508 ; 5.515 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;37.798 ;23.846 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 753 ;15.171 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;16.413 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 635 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3022 ; 0.005 ; 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): 2492 ; 1.049 ; 3.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4027 ; 3.281 ;50.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1541 ; 7.613 ;50.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1435 ; 1.303 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 99999 A 99999 1 REMARK 3 1 B 99999 B 99999 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1942 ; 3.120 ; 5.000 REMARK 3 TIGHT THERMAL 1 A (A**2): 1942 ; 3.320 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 246 REMARK 3 RESIDUE RANGE : A 300 A 301 REMARK 3 RESIDUE RANGE : A 259 A 383 REMARK 3 ORIGIN FOR THE GROUP (A): -14.3816 13.6274 -22.3931 REMARK 3 T TENSOR REMARK 3 T11: 0.0210 T22: 0.0117 REMARK 3 T33: 0.0199 T12: 0.0033 REMARK 3 T13: 0.0091 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 0.2204 L22: 0.5180 REMARK 3 L33: 1.3226 L12: 0.1880 REMARK 3 L13: 0.4930 L23: 0.6670 REMARK 3 S TENSOR REMARK 3 S11: -0.0051 S12: -0.0054 S13: -0.0059 REMARK 3 S21: -0.0113 S22: 0.0127 S23: 0.0220 REMARK 3 S31: -0.0405 S32: -0.0118 S33: -0.0076 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 247 REMARK 3 RESIDUE RANGE : B 300 B 301 REMARK 3 RESIDUE RANGE : B 260 B 387 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6711 -11.5500 -26.0676 REMARK 3 T TENSOR REMARK 3 T11: 0.0133 T22: 0.0107 REMARK 3 T33: 0.0354 T12: 0.0017 REMARK 3 T13: 0.0035 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 0.0097 L22: 0.4884 REMARK 3 L33: 1.4909 L12: 0.0103 REMARK 3 L13: 0.0401 L23: 0.5284 REMARK 3 S TENSOR REMARK 3 S11: 0.0074 S12: -0.0048 S13: -0.0099 REMARK 3 S21: 0.0410 S22: -0.0113 S23: 0.0323 REMARK 3 S31: 0.1101 S32: -0.0096 S33: 0.0039 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 : 1.40 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 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3MF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058466. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33709 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.2000 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) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: PDB ENTRY 3LUF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.1 M TRIS, 0.2 M MGCL2, REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 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 -1 REMARK 465 SER A 0 REMARK 465 LEU A 1 REMARK 465 PHE A 247 REMARK 465 ASN A 248 REMARK 465 SER A 249 REMARK 465 GLU A 250 REMARK 465 GLY A 251 REMARK 465 HIS A 252 REMARK 465 HIS A 253 REMARK 465 HIS A 254 REMARK 465 HIS A 255 REMARK 465 HIS A 256 REMARK 465 HIS A 257 REMARK 465 MSE B -1 REMARK 465 SER B 0 REMARK 465 LEU B 1 REMARK 465 ASN B 248 REMARK 465 SER B 249 REMARK 465 GLU B 250 REMARK 465 GLY B 251 REMARK 465 HIS B 252 REMARK 465 HIS B 253 REMARK 465 HIS B 254 REMARK 465 HIS B 255 REMARK 465 HIS B 256 REMARK 465 HIS B 257 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 ASP A 207 CG OD1 OD2 REMARK 470 ARG A 209 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 43 CG CD OE1 NE2 REMARK 470 GLU B 84 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 OE2 GLU B 70 O HOH B 362 2.11 REMARK 500 O GLY B 94 O HOH B 287 2.12 REMARK 500 NZ LYS A 195 O HOH A 328 2.18 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 LEU B 96 CB - CG - CD1 ANGL. DEV. = -17.4 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 55 66.47 -107.71 REMARK 500 ALA A 59 71.84 -167.26 REMARK 500 GLU A 179 -52.27 73.65 REMARK 500 THR B 55 74.80 -106.42 REMARK 500 ALA B 59 73.26 -153.29 REMARK 500 GLU B 179 -65.65 71.30 REMARK 500 ASP B 207 -154.70 -131.87 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 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD2 REMARK 620 2 ASP A 53 OD2 88.6 REMARK 620 3 THR A 55 OG1 168.5 92.0 REMARK 620 4 THR A 55 O 90.1 87.0 78.4 REMARK 620 5 HOH A 338 O 87.1 169.6 90.3 83.6 REMARK 620 6 HOH A 340 O 95.0 93.6 96.4 174.8 96.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 300 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 130 OD1 REMARK 620 2 ASP A 174 OD2 88.6 REMARK 620 3 TYR A 176 O 91.2 88.4 REMARK 620 4 HOH A 341 O 168.3 80.6 93.0 REMARK 620 5 HOH A 342 O 87.1 86.5 174.7 87.6 REMARK 620 6 HOH A 343 O 92.5 177.0 94.4 98.0 90.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 10 OD1 REMARK 620 2 ASP B 53 OD2 87.0 REMARK 620 3 THR B 55 O 89.1 86.1 REMARK 620 4 THR B 55 OG1 170.3 97.9 82.9 REMARK 620 5 HOH B 272 O 84.3 171.1 92.0 90.5 REMARK 620 6 HOH B 274 O 94.4 96.4 175.9 93.4 86.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 300 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 130 OD1 REMARK 620 2 ASP B 174 OD2 82.4 REMARK 620 3 TYR B 176 O 84.8 86.7 REMARK 620 4 HOH B 292 O 171.1 90.5 100.3 REMARK 620 5 HOH B 321 O 101.5 176.0 94.3 85.5 REMARK 620 6 HOH B 339 O 83.0 86.8 166.8 91.3 93.0 REMARK 620 N 1 2 3 4 5 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LUF RELATED DB: PDB REMARK 900 RELATED ID: NYSGXRC-11202F RELATED DB: TARGETDB DBREF 3MF4 A 2 249 UNP A4SNL2 A4SNL2_AERS4 2 249 DBREF 3MF4 B 2 249 UNP A4SNL2 A4SNL2_AERS4 2 249 SEQADV 3MF4 MSE A -1 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 SER A 0 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 LEU A 1 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 MSE A 17 UNP A4SNL2 THR 17 ENGINEERED MUTATION SEQADV 3MF4 GLN A 148 UNP A4SNL2 LEU 148 ENGINEERED MUTATION SEQADV 3MF4 ALA A 160 UNP A4SNL2 THR 160 ENGINEERED MUTATION SEQADV 3MF4 HIS A 165 UNP A4SNL2 ASN 165 ENGINEERED MUTATION SEQADV 3MF4 GLU A 250 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 GLY A 251 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS A 252 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS A 253 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS A 254 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS A 255 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS A 256 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS A 257 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 MSE B -1 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 SER B 0 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 LEU B 1 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 MSE B 17 UNP A4SNL2 THR 17 ENGINEERED MUTATION SEQADV 3MF4 GLN B 148 UNP A4SNL2 LEU 148 ENGINEERED MUTATION SEQADV 3MF4 ALA B 160 UNP A4SNL2 THR 160 ENGINEERED MUTATION SEQADV 3MF4 HIS B 165 UNP A4SNL2 ASN 165 ENGINEERED MUTATION SEQADV 3MF4 GLU B 250 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 GLY B 251 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS B 252 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS B 253 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS B 254 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS B 255 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS B 256 UNP A4SNL2 EXPRESSION TAG SEQADV 3MF4 HIS B 257 UNP A4SNL2 EXPRESSION TAG SEQRES 1 A 259 MSE SER LEU LYS GLN LYS ILE LEU ILE VAL GLU ASP SER SEQRES 2 A 259 MSE THR ILE ARG ARG MSE LEU ILE GLN ALA ILE ALA GLN SEQRES 3 A 259 GLN THR GLY LEU GLU ILE ASP ALA PHE ASP THR LEU GLU SEQRES 4 A 259 GLY ALA ARG HIS CYS GLN GLY ASP GLU TYR VAL VAL ALA SEQRES 5 A 259 LEU VAL ASP LEU THR LEU PRO ASP ALA PRO SER GLY GLU SEQRES 6 A 259 ALA VAL LYS VAL LEU LEU GLU ARG GLY LEU PRO VAL VAL SEQRES 7 A 259 ILE LEU THR ALA ASP ILE SER GLU ASP LYS ARG GLU ALA SEQRES 8 A 259 TRP LEU GLU ALA GLY VAL LEU ASP TYR VAL MSE LYS ASP SEQRES 9 A 259 SER ARG HIS SER LEU GLN TYR ALA VAL GLY LEU VAL HIS SEQRES 10 A 259 ARG LEU TYR LEU ASN GLN GLN ILE GLU VAL LEU VAL VAL SEQRES 11 A 259 ASP ASP SER ARG THR SER ARG HIS ARG THR MSE ALA GLN SEQRES 12 A 259 LEU ARG LYS GLN LEU LEU GLN VAL HIS GLU ALA SER HIS SEQRES 13 A 259 ALA ARG GLU ALA LEU ALA THR LEU GLU GLN HIS PRO ALA SEQRES 14 A 259 ILE ARG LEU VAL LEU VAL ASP TYR TYR MSE PRO GLU ILE SEQRES 15 A 259 ASP GLY ILE SER LEU VAL ARG MSE LEU ARG GLU ARG TYR SEQRES 16 A 259 SER LYS GLN GLN LEU ALA ILE ILE GLY ILE SER VAL SER SEQRES 17 A 259 ASP LYS ARG GLY LEU SER ALA ARG TYR LEU LYS GLN GLY SEQRES 18 A 259 ALA ASN ASP PHE LEU ASN GLN PRO PHE GLU PRO GLU GLU SEQRES 19 A 259 LEU GLN CYS ARG VAL SER HIS ASN LEU GLU ALA LEU GLU SEQRES 20 A 259 GLN PHE ASN SER GLU GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 259 MSE SER LEU LYS GLN LYS ILE LEU ILE VAL GLU ASP SER SEQRES 2 B 259 MSE THR ILE ARG ARG MSE LEU ILE GLN ALA ILE ALA GLN SEQRES 3 B 259 GLN THR GLY LEU GLU ILE ASP ALA PHE ASP THR LEU GLU SEQRES 4 B 259 GLY ALA ARG HIS CYS GLN GLY ASP GLU TYR VAL VAL ALA SEQRES 5 B 259 LEU VAL ASP LEU THR LEU PRO ASP ALA PRO SER GLY GLU SEQRES 6 B 259 ALA VAL LYS VAL LEU LEU GLU ARG GLY LEU PRO VAL VAL SEQRES 7 B 259 ILE LEU THR ALA ASP ILE SER GLU ASP LYS ARG GLU ALA SEQRES 8 B 259 TRP LEU GLU ALA GLY VAL LEU ASP TYR VAL MSE LYS ASP SEQRES 9 B 259 SER ARG HIS SER LEU GLN TYR ALA VAL GLY LEU VAL HIS SEQRES 10 B 259 ARG LEU TYR LEU ASN GLN GLN ILE GLU VAL LEU VAL VAL SEQRES 11 B 259 ASP ASP SER ARG THR SER ARG HIS ARG THR MSE ALA GLN SEQRES 12 B 259 LEU ARG LYS GLN LEU LEU GLN VAL HIS GLU ALA SER HIS SEQRES 13 B 259 ALA ARG GLU ALA LEU ALA THR LEU GLU GLN HIS PRO ALA SEQRES 14 B 259 ILE ARG LEU VAL LEU VAL ASP TYR TYR MSE PRO GLU ILE SEQRES 15 B 259 ASP GLY ILE SER LEU VAL ARG MSE LEU ARG GLU ARG TYR SEQRES 16 B 259 SER LYS GLN GLN LEU ALA ILE ILE GLY ILE SER VAL SER SEQRES 17 B 259 ASP LYS ARG GLY LEU SER ALA ARG TYR LEU LYS GLN GLY SEQRES 18 B 259 ALA ASN ASP PHE LEU ASN GLN PRO PHE GLU PRO GLU GLU SEQRES 19 B 259 LEU GLN CYS ARG VAL SER HIS ASN LEU GLU ALA LEU GLU SEQRES 20 B 259 GLN PHE ASN SER GLU GLY HIS HIS HIS HIS HIS HIS MODRES 3MF4 MSE A 12 MET SELENOMETHIONINE MODRES 3MF4 MSE A 17 MET SELENOMETHIONINE MODRES 3MF4 MSE A 100 MET SELENOMETHIONINE MODRES 3MF4 MSE A 139 MET SELENOMETHIONINE MODRES 3MF4 MSE A 177 MET SELENOMETHIONINE MODRES 3MF4 MSE A 188 MET SELENOMETHIONINE MODRES 3MF4 MSE B 12 MET SELENOMETHIONINE MODRES 3MF4 MSE B 17 MET SELENOMETHIONINE MODRES 3MF4 MSE B 100 MET SELENOMETHIONINE MODRES 3MF4 MSE B 139 MET SELENOMETHIONINE MODRES 3MF4 MSE B 177 MET SELENOMETHIONINE MODRES 3MF4 MSE B 188 MET SELENOMETHIONINE HET MSE A 12 13 HET MSE A 17 8 HET MSE A 100 8 HET MSE A 139 8 HET MSE A 177 8 HET MSE A 188 8 HET MSE B 12 8 HET MSE B 17 8 HET MSE B 100 8 HET MSE B 139 8 HET MSE B 177 8 HET MSE B 188 8 HET MG A 300 1 HET MG A 301 1 HET MG B 300 1 HET MG B 301 1 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 3 MG 4(MG 2+) FORMUL 7 HOH *249(H2 O) HELIX 1 1 SER A 11 GLY A 27 1 17 HELIX 2 2 LEU A 36 ARG A 40 5 5 HELIX 3 3 GLY A 62 ARG A 71 1 10 HELIX 4 4 SER A 83 ALA A 93 1 11 HELIX 5 5 SER A 103 GLN A 108 1 6 HELIX 6 6 GLN A 108 GLN A 121 1 14 HELIX 7 7 SER A 131 LYS A 144 1 14 HELIX 8 8 HIS A 154 HIS A 165 1 12 HELIX 9 9 ASP A 181 GLU A 191 1 11 HELIX 10 10 GLY A 210 GLN A 218 1 9 HELIX 11 11 GLU A 229 GLN A 246 1 18 HELIX 12 12 SER B 11 THR B 26 1 16 HELIX 13 13 LEU B 36 ARG B 40 5 5 HELIX 14 14 GLU B 63 ARG B 71 1 9 HELIX 15 15 ASP B 85 GLU B 92 1 8 HELIX 16 16 SER B 103 GLN B 121 1 19 HELIX 17 17 SER B 131 LYS B 144 1 14 HELIX 18 18 HIS B 154 HIS B 165 1 12 HELIX 19 19 ASP B 181 GLU B 191 1 11 HELIX 20 20 GLY B 210 GLN B 218 1 9 HELIX 21 21 GLU B 229 PHE B 247 1 19 SHEET 1 A 5 GLU A 29 PHE A 33 0 SHEET 2 A 5 LYS A 4 VAL A 8 1 N ILE A 7 O PHE A 33 SHEET 3 A 5 TYR A 47 ASP A 53 1 O LEU A 51 N LEU A 6 SHEET 4 A 5 VAL A 75 THR A 79 1 O LEU A 78 N VAL A 52 SHEET 5 A 5 ASP A 97 MSE A 100 1 O VAL A 99 N ILE A 77 SHEET 1 B 5 GLN A 148 ALA A 152 0 SHEET 2 B 5 GLU A 124 VAL A 128 1 N VAL A 125 O HIS A 150 SHEET 3 B 5 ILE A 168 VAL A 173 1 O LEU A 172 N LEU A 126 SHEET 4 B 5 ALA A 199 SER A 204 1 O ILE A 203 N VAL A 173 SHEET 5 B 5 ASP A 222 ASN A 225 1 O LEU A 224 N SER A 204 SHEET 1 C 5 GLU B 29 PHE B 33 0 SHEET 2 C 5 LYS B 4 VAL B 8 1 N ILE B 5 O GLU B 29 SHEET 3 C 5 TYR B 47 ASP B 53 1 O VAL B 48 N LYS B 4 SHEET 4 C 5 VAL B 75 THR B 79 1 O VAL B 76 N ALA B 50 SHEET 5 C 5 ASP B 97 MSE B 100 1 O VAL B 99 N ILE B 77 SHEET 1 D 5 GLN B 148 ALA B 152 0 SHEET 2 D 5 GLU B 124 VAL B 128 1 N VAL B 125 O HIS B 150 SHEET 3 D 5 LEU B 170 ASP B 174 1 O LEU B 172 N VAL B 128 SHEET 4 D 5 ALA B 199 SER B 204 1 O ILE B 203 N VAL B 173 SHEET 5 D 5 ASP B 222 ASN B 225 1 O ASP B 222 N GLY B 202 LINK C SER A 11 N MSE A 12 1555 1555 1.34 LINK C MSE A 12 N THR A 13 1555 1555 1.33 LINK C ARG A 16 N MSE A 17 1555 1555 1.34 LINK C MSE A 17 N LEU A 18 1555 1555 1.33 LINK C VAL A 99 N MSE A 100 1555 1555 1.33 LINK C MSE A 100 N LYS A 101 1555 1555 1.32 LINK C THR A 138 N MSE A 139 1555 1555 1.33 LINK C MSE A 139 N ALA A 140 1555 1555 1.34 LINK C TYR A 176 N MSE A 177 1555 1555 1.33 LINK C MSE A 177 N PRO A 178 1555 1555 1.35 LINK C AARG A 187 N MSE A 188 1555 1555 1.33 LINK C BARG A 187 N MSE A 188 1555 1555 1.33 LINK C MSE A 188 N LEU A 189 1555 1555 1.33 LINK C SER B 11 N MSE B 12 1555 1555 1.33 LINK C MSE B 12 N THR B 13 1555 1555 1.33 LINK C ARG B 16 N MSE B 17 1555 1555 1.33 LINK C MSE B 17 N LEU B 18 1555 1555 1.33 LINK C VAL B 99 N MSE B 100 1555 1555 1.34 LINK C MSE B 100 N LYS B 101 1555 1555 1.33 LINK C THR B 138 N MSE B 139 1555 1555 1.33 LINK C MSE B 139 N ALA B 140 1555 1555 1.33 LINK C TYR B 176 N MSE B 177 1555 1555 1.33 LINK C MSE B 177 N PRO B 178 1555 1555 1.35 LINK C ARG B 187 N MSE B 188 1555 1555 1.35 LINK C MSE B 188 N LEU B 189 1555 1555 1.34 LINK OD2 ASP A 10 MG MG A 301 1555 1555 2.01 LINK OD2 ASP A 53 MG MG A 301 1555 1555 2.06 LINK OG1 THR A 55 MG MG A 301 1555 1555 2.12 LINK O THR A 55 MG MG A 301 1555 1555 2.15 LINK OD1 ASP A 130 MG MG A 300 1555 1555 2.08 LINK OD2 ASP A 174 MG MG A 300 1555 1555 2.08 LINK O TYR A 176 MG MG A 300 1555 1555 2.03 LINK MG MG A 300 O HOH A 341 1555 1555 2.06 LINK MG MG A 300 O HOH A 342 1555 1555 2.02 LINK MG MG A 300 O HOH A 343 1555 1555 1.81 LINK MG MG A 301 O HOH A 338 1555 1555 2.19 LINK MG MG A 301 O HOH A 340 1555 1555 1.96 LINK OD1 ASP B 10 MG MG B 301 1555 1555 2.09 LINK OD2 ASP B 53 MG MG B 301 1555 1555 1.93 LINK O THR B 55 MG MG B 301 1555 1555 1.99 LINK OG1 THR B 55 MG MG B 301 1555 1555 2.00 LINK OD1 ASP B 130 MG MG B 300 1555 1555 2.09 LINK OD2 ASP B 174 MG MG B 300 1555 1555 2.06 LINK O TYR B 176 MG MG B 300 1555 1555 2.11 LINK O HOH B 272 MG MG B 301 1555 1555 2.18 LINK O HOH B 274 MG MG B 301 1555 1555 2.09 LINK O HOH B 292 MG MG B 300 1555 1555 2.07 LINK MG MG B 300 O HOH B 321 1555 1555 1.91 LINK MG MG B 300 O HOH B 339 1555 1555 2.14 CISPEP 1 GLN A 226 PRO A 227 0 -4.26 CISPEP 2 GLN B 226 PRO B 227 0 -0.36 SITE 1 AC1 6 ASP A 130 ASP A 174 TYR A 176 HOH A 341 SITE 2 AC1 6 HOH A 342 HOH A 343 SITE 1 AC2 6 ASP A 10 ASP A 53 THR A 55 GLU A 191 SITE 2 AC2 6 HOH A 338 HOH A 340 SITE 1 AC3 6 ASP B 130 ASP B 174 TYR B 176 HOH B 292 SITE 2 AC3 6 HOH B 321 HOH B 339 SITE 1 AC4 6 ASP B 10 ASP B 53 THR B 55 GLU B 191 SITE 2 AC4 6 HOH B 272 HOH B 274 CRYST1 40.919 53.269 57.908 61.95 81.09 78.76 P 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 0.024439 -0.004857 -0.001824 0.00000 SCALE2 0.000000 0.019140 -0.009758 0.00000 SCALE3 0.000000 0.000000 0.019620 0.00000