HEADER OXIDOREDUCTASE 15-MAR-06 2GD9 TITLE CRYSTAL STRUCTURE OF A PUTATIVE DIHYDROFOLATE REDUCTASE (BSU40760, TITLE 2 YYAP) FROM BACILLUS SUBTILIS AT 2.30 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YYAP; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: YYAP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 25-JAN-23 2GD9 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2GD9 1 VERSN REVDAT 3 23-MAR-11 2GD9 1 HEADER TITLE KEYWDS REVDAT 2 24-FEB-09 2GD9 1 VERSN REVDAT 1 28-MAR-06 2GD9 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF (2636623) FROM BACILLUS SUBTILIS AT JRNL TITL 2 2.30 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 26334 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1364 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1824 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2825 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 155 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) : 31.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77000 REMARK 3 B22 (A**2) : 0.77000 REMARK 3 B33 (A**2) : -1.54000 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): 0.236 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.207 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.157 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.184 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2927 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2688 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3949 ; 1.524 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6244 ; 0.855 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 347 ; 6.871 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;40.179 ;24.710 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 531 ;16.373 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;12.522 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 436 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3166 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 596 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 455 ; 0.164 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2620 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1325 ; 0.170 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1724 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 146 ; 0.179 ; 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): 16 ; 0.168 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 84 ; 0.197 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.150 ; 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): 1777 ; 0.708 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 722 ; 0.126 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2790 ; 1.170 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1342 ; 1.607 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1157 ; 2.483 ; 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 : 3 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 0 A 55 5 REMARK 3 1 B 0 B 55 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 328 ; 0.130 ; 0.500 REMARK 3 LOOSE POSITIONAL 1 A (A): 521 ; 0.540 ; 5.000 REMARK 3 MEDIUM THERMAL 1 A (A**2): 328 ; 0.450 ; 2.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 521 ; 0.970 ;10.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 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 74 A 86 5 REMARK 3 1 B 74 B 86 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 78 ; 0.220 ; 0.500 REMARK 3 LOOSE POSITIONAL 2 A (A): 146 ; 0.810 ; 5.000 REMARK 3 MEDIUM THERMAL 2 A (A**2): 78 ; 0.960 ; 2.000 REMARK 3 LOOSE THERMAL 2 A (A**2): 146 ; 1.950 ;10.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 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 106 A 186 5 REMARK 3 1 B 106 B 187 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 3 A (A): 472 ; 0.160 ; 0.500 REMARK 3 LOOSE POSITIONAL 3 A (A): 768 ; 0.450 ; 5.000 REMARK 3 MEDIUM THERMAL 3 A (A**2): 472 ; 0.690 ; 2.000 REMARK 3 LOOSE THERMAL 3 A (A**2): 768 ; 1.090 ;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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 186 REMARK 3 ORIGIN FOR THE GROUP (A): 17.2326 28.0834 83.6810 REMARK 3 T TENSOR REMARK 3 T11: -0.0571 T22: -0.0049 REMARK 3 T33: -0.0628 T12: -0.0538 REMARK 3 T13: 0.0058 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 1.1127 L22: 0.4902 REMARK 3 L33: 2.2774 L12: -0.1111 REMARK 3 L13: -0.1891 L23: -0.0655 REMARK 3 S TENSOR REMARK 3 S11: 0.0122 S12: 0.0528 S13: -0.0640 REMARK 3 S21: -0.0263 S22: 0.0276 S23: 0.0585 REMARK 3 S31: 0.2152 S32: -0.2131 S33: -0.0397 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 : B 0 B 186 REMARK 3 ORIGIN FOR THE GROUP (A): 28.3700 47.0015 59.8926 REMARK 3 T TENSOR REMARK 3 T11: 0.0017 T22: -0.0903 REMARK 3 T33: -0.0488 T12: 0.0221 REMARK 3 T13: -0.0094 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.5083 L22: 1.5452 REMARK 3 L33: 2.5250 L12: 0.3384 REMARK 3 L13: -0.4054 L23: -0.7035 REMARK 3 S TENSOR REMARK 3 S11: 0.0562 S12: -0.0376 S13: 0.0997 REMARK 3 S21: 0.0151 S22: 0.0281 S23: 0.1701 REMARK 3 S31: -0.2930 S32: -0.1067 S33: -0.0843 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: REMARK 3 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE REMARK 3 SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR REMARK 3 THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. REMARK 3 3. RESIDUES 63-74 OF BOTH CHAINS, AND 90-100 OF CHAIN B WERE REMARK 3 DISORDERED AND NOT MODELED. REMARK 3 4. THE MAINCHAIN AND SIDECHAIN POSITIONS OF B186 REMARK 3 WERE MODELED BASED ON THE POSITION OF THE A CHAIN. REMARK 3 THE C-TERMINAL REGION OF BOTH MONOMERS LIES ON A REMARK 3 NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS, MAKING THE REMARK 3 INTERPRETATION OF THE DISORDERED DENSITY IN THIS AREA REMARK 3 PROBLEMATIC. REMARK 3 5. GLY125-126 IS IN THE CIS-CONFORMATION IN BOTH CHAINS. THIS IS REMARK 3 LOCATED IN THE ACTIVE SITE AND IS CONSERVED IN OTHER DIHYDROFOLATE REMARK 3 REDUCTAESES. REMARK 3 6. PO4 AND CL ARE MODELED IN THE PUTATIVE ACTIVE SITE. REMARK 3 7. EDO MODELED BASED ON CRYO CONDITIONS. REMARK 4 REMARK 4 2GD9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.019859, 0.979718 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26393 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 64.957 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : 0.11400 REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.74700 REMARK 200 R SYM FOR SHELL (I) : 0.74700 REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M (NH4)2HPO4, 20.0% PEG-3350, NO REMARK 280 BUFFER PH 7.9, VAPOR DIFFUSION,SITTING DROP,NANODROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 71.82400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 107.73600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.91200 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: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 ILE A 64 REMARK 465 PRO A 65 REMARK 465 LYS A 66 REMARK 465 ASN A 67 REMARK 465 GLU A 68 REMARK 465 ASP A 69 REMARK 465 PRO A 70 REMARK 465 ASP A 71 REMARK 465 THR A 72 REMARK 465 GLU A 73 REMARK 465 ASN A 187 REMARK 465 GLY A 188 REMARK 465 PRO B 65 REMARK 465 LYS B 66 REMARK 465 ASN B 67 REMARK 465 GLU B 68 REMARK 465 ASP B 69 REMARK 465 PRO B 70 REMARK 465 ASP B 71 REMARK 465 THR B 72 REMARK 465 THR B 91 REMARK 465 GLN B 92 REMARK 465 ASN B 93 REMARK 465 GLU B 94 REMARK 465 ILE B 95 REMARK 465 ASP B 96 REMARK 465 ASN B 97 REMARK 465 GLN B 98 REMARK 465 ALA B 99 REMARK 465 GLY B 188 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 LEU A 5 CG CD1 CD2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 112 CD CE NZ REMARK 470 ARG B 9 CZ NH1 NH2 REMARK 470 ARG B 90 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 112 CE NZ 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 B 143 NE - CZ - NH2 ANGL. DEV. = 3.6 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 GLU A 23 143.33 -171.10 REMARK 500 LEU A 59 -64.55 -91.47 REMARK 500 LYS A 119 -153.58 -98.45 REMARK 500 LYS B 119 -158.51 -84.71 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 CL A 189 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 189 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 192 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 193 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 359096 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED REMARK 999 WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) REMARK 999 FOLLOWED BY THE TARGET SEQUENCE. DBREF 2GD9 A 1 188 UNP P37508 YYAP_BACSU 1 188 DBREF 2GD9 B 1 188 UNP P37508 YYAP_BACSU 1 188 SEQADV 2GD9 GLY A 0 UNP P37508 EXPRESSION TAG SEQADV 2GD9 MSE A 1 UNP P37508 MET 1 MODIFIED RESIDUE SEQADV 2GD9 MSE A 34 UNP P37508 MET 34 MODIFIED RESIDUE SEQADV 2GD9 MSE A 38 UNP P37508 MET 38 MODIFIED RESIDUE SEQADV 2GD9 MSE A 169 UNP P37508 MET 169 MODIFIED RESIDUE SEQADV 2GD9 GLY B 0 UNP P37508 EXPRESSION TAG SEQADV 2GD9 MSE B 1 UNP P37508 MET 1 MODIFIED RESIDUE SEQADV 2GD9 MSE B 34 UNP P37508 MET 34 MODIFIED RESIDUE SEQADV 2GD9 MSE B 38 UNP P37508 MET 38 MODIFIED RESIDUE SEQADV 2GD9 MSE B 169 UNP P37508 MET 169 MODIFIED RESIDUE SEQRES 1 A 189 GLY MSE THR ASN ASN LEU LYS GLN ARG ARG ILE ILE LEU SEQRES 2 A 189 ASP LEU ALA VAL THR LEU ASP GLY PHE ILE GLU GLY LYS SEQRES 3 A 189 ASN GLY GLU VAL ASP TRP CYS ILE MSE ASP PRO ASP MSE SEQRES 4 A 189 GLY PHE THR ASP PHE LEU ASN GLN ILE ASP THR ILE LEU SEQRES 5 A 189 TYR GLY ARG LYS SER PHE ASP LEU TRP GLY GLN TYR ILE SEQRES 6 A 189 PRO LYS ASN GLU ASP PRO ASP THR GLU LYS GLU LEU TRP SEQRES 7 A 189 LYS LEU VAL HIS SER LYS LYS LYS TYR VAL PHE SER ARG SEQRES 8 A 189 THR GLN ASN GLU ILE ASP ASN GLN ALA ILE PHE ILE ASN SEQRES 9 A 189 ASP ASN ILE LEU GLU GLU VAL ASN LYS LEU LYS LYS ASN SEQRES 10 A 189 PRO GLY LYS ASP ILE TRP LEU TYR GLY GLY ALA SER LEU SEQRES 11 A 189 ILE THR THR PHE ILE ASN LEU GLY LEU VAL ASP GLU PHE SEQRES 12 A 189 ARG LEU SER ILE HIS PRO VAL VAL LEU GLY GLU GLY LYS SEQRES 13 A 189 PRO LEU PHE ILE ASP VAL LYS GLN ARG ILE ASN LEU LYS SEQRES 14 A 189 MSE VAL ASN THR ARG THR PHE SER SER GLY VAL VAL GLN SEQRES 15 A 189 ILE VAL TYR HIS TRP ASN GLY SEQRES 1 B 189 GLY MSE THR ASN ASN LEU LYS GLN ARG ARG ILE ILE LEU SEQRES 2 B 189 ASP LEU ALA VAL THR LEU ASP GLY PHE ILE GLU GLY LYS SEQRES 3 B 189 ASN GLY GLU VAL ASP TRP CYS ILE MSE ASP PRO ASP MSE SEQRES 4 B 189 GLY PHE THR ASP PHE LEU ASN GLN ILE ASP THR ILE LEU SEQRES 5 B 189 TYR GLY ARG LYS SER PHE ASP LEU TRP GLY GLN TYR ILE SEQRES 6 B 189 PRO LYS ASN GLU ASP PRO ASP THR GLU LYS GLU LEU TRP SEQRES 7 B 189 LYS LEU VAL HIS SER LYS LYS LYS TYR VAL PHE SER ARG SEQRES 8 B 189 THR GLN ASN GLU ILE ASP ASN GLN ALA ILE PHE ILE ASN SEQRES 9 B 189 ASP ASN ILE LEU GLU GLU VAL ASN LYS LEU LYS LYS ASN SEQRES 10 B 189 PRO GLY LYS ASP ILE TRP LEU TYR GLY GLY ALA SER LEU SEQRES 11 B 189 ILE THR THR PHE ILE ASN LEU GLY LEU VAL ASP GLU PHE SEQRES 12 B 189 ARG LEU SER ILE HIS PRO VAL VAL LEU GLY GLU GLY LYS SEQRES 13 B 189 PRO LEU PHE ILE ASP VAL LYS GLN ARG ILE ASN LEU LYS SEQRES 14 B 189 MSE VAL ASN THR ARG THR PHE SER SER GLY VAL VAL GLN SEQRES 15 B 189 ILE VAL TYR HIS TRP ASN GLY MODRES 2GD9 MSE A 1 MET SELENOMETHIONINE MODRES 2GD9 MSE A 34 MET SELENOMETHIONINE MODRES 2GD9 MSE A 38 MET SELENOMETHIONINE MODRES 2GD9 MSE A 169 MET SELENOMETHIONINE MODRES 2GD9 MSE B 1 MET SELENOMETHIONINE MODRES 2GD9 MSE B 34 MET SELENOMETHIONINE MODRES 2GD9 MSE B 38 MET SELENOMETHIONINE MODRES 2GD9 MSE B 169 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 34 8 HET MSE A 38 8 HET MSE A 169 8 HET MSE B 1 8 HET MSE B 34 8 HET MSE B 38 8 HET MSE B 169 8 HET CL A 189 1 HET PO4 A 190 5 HET EDO A 191 4 HET EDO A 192 4 HET EDO A 193 4 HET PO4 B 189 5 HET EDO B 190 4 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION HETNAM PO4 PHOSPHATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 CL CL 1- FORMUL 4 PO4 2(O4 P 3-) FORMUL 5 EDO 4(C2 H6 O2) FORMUL 10 HOH *155(H2 O) HELIX 1 1 GLY A 39 GLN A 46 1 8 HELIX 2 2 ARG A 54 GLY A 61 1 8 HELIX 3 3 GLU A 75 LYS A 83 1 9 HELIX 4 4 ILE A 102 ASN A 116 1 15 HELIX 5 5 GLY A 126 LEU A 136 1 11 HELIX 6 6 ASP B 35 MSE B 38 5 4 HELIX 7 7 GLY B 39 GLN B 46 1 8 HELIX 8 8 ARG B 54 GLY B 61 1 8 HELIX 9 9 GLU B 73 SER B 82 1 10 HELIX 10 10 ILE B 102 LYS B 115 1 14 HELIX 11 11 GLY B 126 LEU B 136 1 11 SHEET 1 A 7 LYS A 84 PHE A 88 0 SHEET 2 A 7 ILE A 47 GLY A 53 1 N ASP A 48 O LYS A 84 SHEET 3 A 7 ASP A 120 GLY A 125 1 O TRP A 122 N LEU A 51 SHEET 4 A 7 ILE A 10 VAL A 16 1 N ILE A 11 O ILE A 121 SHEET 5 A 7 GLU A 141 ILE A 146 1 O ARG A 143 N LEU A 12 SHEET 6 A 7 VAL A 180 HIS A 185 -1 O ILE A 182 N LEU A 144 SHEET 7 A 7 LYS A 168 THR A 174 -1 N VAL A 170 O VAL A 183 SHEET 1 B 2 PHE A 21 GLU A 23 0 SHEET 2 B 2 LYS A 155 PRO A 156 -1 O LYS A 155 N ILE A 22 SHEET 1 C 2 THR A 91 ASN A 93 0 SHEET 2 C 2 GLN A 98 ILE A 100 -1 O GLN A 98 N ASN A 93 SHEET 1 D 2 VAL A 149 VAL A 150 0 SHEET 2 D 2 ILE B 165 ASN B 166 -1 O ILE B 165 N VAL A 150 SHEET 1 E 2 ILE A 165 ASN A 166 0 SHEET 2 E 2 VAL B 149 VAL B 150 -1 O VAL B 150 N ILE A 165 SHEET 1 F 7 LYS B 84 PHE B 88 0 SHEET 2 F 7 ILE B 47 GLY B 53 1 N TYR B 52 O TYR B 86 SHEET 3 F 7 ASP B 120 GLY B 125 1 O TRP B 122 N LEU B 51 SHEET 4 F 7 ILE B 10 THR B 17 1 N ILE B 11 O ILE B 121 SHEET 5 F 7 GLU B 141 HIS B 147 1 O ARG B 143 N LEU B 12 SHEET 6 F 7 VAL B 180 HIS B 185 -1 O VAL B 180 N ILE B 146 SHEET 7 F 7 LYS B 168 THR B 174 -1 N VAL B 170 O VAL B 183 SHEET 1 G 2 PHE B 21 GLU B 23 0 SHEET 2 G 2 LYS B 155 PRO B 156 -1 O LYS B 155 N ILE B 22 LINK C GLY A 0 N MSE A 1 1555 1555 1.32 LINK C MSE A 1 N THR A 2 1555 1555 1.32 LINK C ILE A 33 N MSE A 34 1555 1555 1.33 LINK C MSE A 34 N ASP A 35 1555 1555 1.32 LINK C ASP A 37 N MSE A 38 1555 1555 1.34 LINK C MSE A 38 N GLY A 39 1555 1555 1.34 LINK C LYS A 168 N MSE A 169 1555 1555 1.33 LINK C MSE A 169 N VAL A 170 1555 1555 1.34 LINK C GLY B 0 N MSE B 1 1555 1555 1.33 LINK C MSE B 1 N THR B 2 1555 1555 1.33 LINK C ILE B 33 N MSE B 34 1555 1555 1.32 LINK C MSE B 34 N ASP B 35 1555 1555 1.32 LINK C ASP B 37 N MSE B 38 1555 1555 1.34 LINK C MSE B 38 N GLY B 39 1555 1555 1.34 LINK C LYS B 168 N MSE B 169 1555 1555 1.33 LINK C MSE B 169 N VAL B 170 1555 1555 1.34 CISPEP 1 GLY A 125 GLY A 126 0 2.20 CISPEP 2 GLY B 125 GLY B 126 0 0.83 SITE 1 AC1 5 GLY A 53 LYS A 55 SER A 56 ARG A 90 SITE 2 AC1 5 GLY A 126 SITE 1 AC2 8 LYS A 55 ARG A 90 SER A 128 LYS A 155 SITE 2 AC2 8 EDO A 192 HOH A 200 HOH A 265 HOH A 268 SITE 1 AC3 6 LYS B 55 ALA B 127 SER B 128 LYS B 155 SITE 2 AC3 6 HOH B 228 HOH B 251 SITE 1 AC4 5 ILE A 22 GLU A 23 ILE A 130 HOH A 229 SITE 2 AC4 5 HOH A 276 SITE 1 AC5 3 LYS A 155 PO4 A 190 HOH A 256 SITE 1 AC6 5 LEU B 14 GLU B 23 TYR B 124 ALA B 127 SITE 2 AC6 5 HOH B 252 SITE 1 AC7 4 THR A 17 LEU A 18 THR B 17 LEU B 18 CRYST1 64.915 64.915 143.648 90.00 90.00 90.00 P 43 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 0.015410 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015410 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006960 0.00000