HEADER TRANSFERASE 09-MAR-09 3GJU TITLE CRYSTAL STRUCTURE OF A PUTATIVE AMINOTRANSFERASE (MLL7127) FROM TITLE 2 MESORHIZOBIUM LOTI MAFF303099 AT 1.55 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE AMINOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESORHIZOBIUM LOTI; SOURCE 3 ORGANISM_TAXID: 266835; SOURCE 4 STRAIN: MAFF303099; SOURCE 5 GENE: MLL7127, NP_107505.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PYRIDOXAL PHOSPHATE, PLP-DEPENDENT TRANSFERASE-LIKE FOLD, STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI-2, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 24-JUL-19 3GJU 1 REMARK LINK REVDAT 4 01-NOV-17 3GJU 1 REMARK REVDAT 3 13-JUL-11 3GJU 1 VERSN REVDAT 2 23-MAR-11 3GJU 1 HEADER TITLE KEYWDS REVDAT 1 17-MAR-09 3GJU 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE AMINOTRANSFERASE (NP_107505.1) JRNL TITL 2 FROM MESORHIZOBIUM LOTI AT 1.55 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 61444 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3122 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4065 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 227 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3487 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 458 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 13.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -0.90000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.070 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.260 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3697 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2459 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5043 ; 1.533 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6008 ; 0.990 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 490 ; 6.036 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;36.833 ;23.742 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 596 ;12.736 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;15.410 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 550 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4193 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 757 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2311 ; 1.453 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 965 ; 0.471 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3709 ; 2.141 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1386 ; 3.723 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1318 ; 5.059 ;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 : 1 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 457 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4846 18.6939 21.9808 REMARK 3 T TENSOR REMARK 3 T11: 0.0055 T22: 0.0149 REMARK 3 T33: 0.0117 T12: 0.0010 REMARK 3 T13: 0.0047 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.2474 L22: 0.1991 REMARK 3 L33: 0.2405 L12: 0.0717 REMARK 3 L13: 0.0980 L23: -0.0059 REMARK 3 S TENSOR REMARK 3 S11: -0.0195 S12: 0.0212 S13: -0.0061 REMARK 3 S21: -0.0213 S22: 0.0229 S23: 0.0066 REMARK 3 S31: -0.0128 S32: -0.0289 S33: -0.0034 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS REMARK 3 ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED REMARK 3 SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. 2-METHYL- REMARK 3 2,4-PENTANEDIOL (MPD) FROM THE CRYSTALLIZATION CONDITION HAS REMARK 3 BEEN MODELED IN THE SOLVENT STRUCTURE. 5. PYRIDOXAL PHOSPHATE IN REMARK 3 DUAL CONFORMATION AS FREE PLP AND COVALENTLY ATTACHED TO LYS289 REMARK 3 (LLP) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON REMARK 3 DIFFERENCE DENSITY AND OMIT MAPS AND STRUCTURAL SIMILARITY TO REMARK 3 PLP-DEPENDENT AMINOTRANSFERASES. 6. RESIDUE ALA288 IS PRESENT IN REMARK 3 THE VICINITY OF THE PUTATIVE ACTIVE SITE AND IS A RAMACHANDRAN REMARK 3 OUTLIER. THIS COULD HAVE SOME FUNCTIONAL SIGNIFICANCE. REMARK 4 REMARK 4 3GJU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051950. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162, 0.97941, 0.97954 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61448 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 28.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 59.1% 2-METHYL-2,4 REMARK 280 -PENTANEDIOL, 0.1M BICINE PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 56.61200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.78850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.61200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.78850 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 300 REMARK: CRYSTAL PACKING ANALYSIS SUGGESTS THAT A DIMER IS THE REMARK 300 STABLE OLIGOMERIC FORM IN SOLUTION. 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: 10750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 57.70019 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.80363 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 496 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 458 REMARK 465 LEU A 459 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 80 CD CE NZ REMARK 470 GLU A 142 CD OE1 OE2 REMARK 470 LYS A 281 CE NZ REMARK 470 ARG A 306 CD NE CZ NH1 NH2 REMARK 470 LYS A 453 CD CE NZ 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 OD2 ASP A 276 O HOH A 918 2.09 REMARK 500 O HOH A 661 O HOH A 796 2.15 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 NH2 ARG A 177 O HOH A 791 2656 2.13 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 82 96.97 -162.69 REMARK 500 SER A 148 -163.03 -107.99 REMARK 500 PRO A 179 41.55 -103.49 REMARK 500 THR A 183 -168.17 -100.63 REMARK 500 ILE A 235 70.30 49.54 REMARK 500 ALA A 288 -144.31 -170.74 REMARK 500 ALA A 288 -144.44 -170.74 REMARK 500 LLP A 289 -97.38 37.92 REMARK 500 LYS A 289 -99.79 38.64 REMARK 500 MSE A 382 43.40 -96.38 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 PLP A 460 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 461 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 462 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 390987 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3GJU A 1 459 UNP Q987B2 Q987B2_RHILO 1 459 SEQADV 3GJU GLY A 0 UNP Q987B2 LEADER SEQUENCE SEQADV 3GJU LYS A 289 UNP Q987B2 LLP 289 MICROHETEROGENEITY SEQRES 1 A 460 GLY MSE LEU ASN GLN SER ASN GLU LEU ASN ALA TRP ASP SEQRES 2 A 460 ARG ASP HIS PHE PHE HIS PRO SER THR HIS MSE GLY THR SEQRES 3 A 460 HIS ALA ARG GLY GLU SER PRO THR ARG ILE MSE ALA GLY SEQRES 4 A 460 GLY GLU GLY VAL THR VAL TRP ASP ASN ASN GLY ARG LYS SEQRES 5 A 460 SER ILE ASP ALA PHE ALA GLY LEU TYR CYS VAL ASN VAL SEQRES 6 A 460 GLY TYR GLY ARG GLN LYS ILE ALA ASP ALA ILE ALA THR SEQRES 7 A 460 GLN ALA LYS ASN LEU ALA TYR TYR HIS ALA TYR VAL GLY SEQRES 8 A 460 HIS GLY THR GLU ALA SER ILE THR LEU ALA LYS MSE ILE SEQRES 9 A 460 ILE ASP ARG ALA PRO LYS GLY MSE SER ARG VAL TYR PHE SEQRES 10 A 460 GLY LEU SER GLY SER ASP ALA ASN GLU THR ASN ILE LYS SEQRES 11 A 460 LEU ILE TRP TYR TYR ASN ASN VAL LEU GLY ARG PRO GLU SEQRES 12 A 460 LYS LYS LYS ILE ILE SER ARG TRP ARG GLY TYR HIS GLY SEQRES 13 A 460 SER GLY VAL MSE THR GLY SER LEU THR GLY LEU ASP LEU SEQRES 14 A 460 PHE HIS ASN ALA PHE ASP LEU PRO ARG ALA PRO VAL LEU SEQRES 15 A 460 HIS THR GLU ALA PRO TYR TYR PHE ARG ARG THR ASP ARG SEQRES 16 A 460 SER MSE SER GLU GLU GLN PHE SER GLN HIS CYS ALA ASP SEQRES 17 A 460 LYS LEU GLU GLU MSE ILE LEU ALA GLU GLY PRO GLU THR SEQRES 18 A 460 ILE ALA ALA PHE ILE GLY GLU PRO ILE LEU GLY THR GLY SEQRES 19 A 460 GLY ILE VAL PRO PRO PRO ALA GLY TYR TRP GLU LYS ILE SEQRES 20 A 460 GLN ALA VAL LEU LYS LYS TYR ASP VAL LEU LEU VAL ALA SEQRES 21 A 460 ASP GLU VAL VAL THR GLY PHE GLY ARG LEU GLY THR MSE SEQRES 22 A 460 PHE GLY SER ASP HIS TYR GLY ILE LYS PRO ASP LEU ILE SEQRES 23 A 460 THR ILE ALA LLP GLY LEU THR SER ALA TYR ALA PRO LEU SEQRES 24 A 460 SER GLY VAL ILE VAL ALA ASP ARG VAL TRP GLN VAL LEU SEQRES 25 A 460 VAL GLN GLY SER ASP LYS LEU GLY SER LEU GLY HIS GLY SEQRES 26 A 460 TRP THR TYR SER ALA HIS PRO ILE CYS VAL ALA ALA GLY SEQRES 27 A 460 VAL ALA ASN LEU GLU LEU ILE ASP GLU MSE ASP LEU VAL SEQRES 28 A 460 THR ASN ALA GLY GLU THR GLY ALA TYR PHE ARG ALA GLU SEQRES 29 A 460 LEU ALA LYS ALA VAL GLY GLY HIS LYS ASN VAL GLY GLU SEQRES 30 A 460 VAL ARG GLY ASP GLY MSE LEU ALA ALA VAL GLU PHE VAL SEQRES 31 A 460 ALA ASP LYS ASP ASP ARG VAL PHE PHE ASP ALA SER GLN SEQRES 32 A 460 LYS ILE GLY PRO GLN VAL ALA THR ALA LEU ALA ALA SER SEQRES 33 A 460 GLY VAL ILE GLY ARG ALA MSE PRO GLN GLY ASP ILE LEU SEQRES 34 A 460 GLY PHE ALA PRO PRO LEU CYS LEU THR ARG GLU GLN ALA SEQRES 35 A 460 ASP ILE VAL VAL SER LYS THR ALA ASP ALA VAL LYS SER SEQRES 36 A 460 VAL PHE ALA ASN LEU MODRES 3GJU MSE A 1 MET SELENOMETHIONINE MODRES 3GJU MSE A 23 MET SELENOMETHIONINE MODRES 3GJU MSE A 36 MET SELENOMETHIONINE MODRES 3GJU MSE A 102 MET SELENOMETHIONINE MODRES 3GJU MSE A 111 MET SELENOMETHIONINE MODRES 3GJU MSE A 159 MET SELENOMETHIONINE MODRES 3GJU MSE A 196 MET SELENOMETHIONINE MODRES 3GJU MSE A 212 MET SELENOMETHIONINE MODRES 3GJU MSE A 272 MET SELENOMETHIONINE MODRES 3GJU LLP A 289 LYS MODRES 3GJU MSE A 347 MET SELENOMETHIONINE MODRES 3GJU MSE A 382 MET SELENOMETHIONINE MODRES 3GJU MSE A 422 MET SELENOMETHIONINE HET MSE A 1 13 HET MSE A 23 8 HET MSE A 36 13 HET MSE A 102 8 HET MSE A 111 13 HET MSE A 159 13 HET MSE A 196 8 HET MSE A 212 8 HET MSE A 272 8 HET LLP A 289 24 HET MSE A 347 8 HET MSE A 382 8 HET MSE A 422 8 HET PLP A 460 16 HET MPD A 461 8 HET MPD A 462 8 HETNAM MSE SELENOMETHIONINE HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 MPD 2(C6 H14 O2) FORMUL 5 HOH *458(H2 O) HELIX 1 1 GLU A 7 PHE A 16 1 10 HELIX 2 2 HIS A 22 ARG A 28 1 7 HELIX 3 3 PHE A 56 CYS A 61 1 6 HELIX 4 4 ARG A 68 ALA A 83 1 16 HELIX 5 5 THR A 93 ALA A 107 1 15 HELIX 6 6 SER A 119 LEU A 138 1 20 HELIX 7 7 GLY A 157 THR A 164 1 8 HELIX 8 8 LEU A 166 HIS A 170 5 5 HELIX 9 9 TYR A 187 ARG A 191 5 5 HELIX 10 10 SER A 197 GLY A 217 1 21 HELIX 11 11 GLY A 241 TYR A 253 1 13 HELIX 12 12 PHE A 273 GLY A 279 1 7 HELIX 13 13 ALA A 288 THR A 292 5 5 HELIX 14 14 ASP A 305 GLY A 319 1 15 HELIX 15 15 HIS A 330 MSE A 347 1 18 HELIX 16 16 ASP A 348 GLY A 369 1 22 HELIX 17 17 ASP A 399 GLN A 402 5 4 HELIX 18 18 LYS A 403 SER A 415 1 13 HELIX 19 19 THR A 437 ALA A 457 1 21 SHEET 1 A 4 MSE A 36 GLU A 40 0 SHEET 2 A 4 THR A 43 ASP A 46 -1 O TRP A 45 N ALA A 37 SHEET 3 A 4 LYS A 51 ASP A 54 -1 O SER A 52 N VAL A 44 SHEET 4 A 4 VAL A 417 ILE A 418 1 O ILE A 418 N ILE A 53 SHEET 1 B 7 MSE A 111 GLY A 117 0 SHEET 2 B 7 SER A 299 ALA A 304 -1 O VAL A 303 N ARG A 113 SHEET 3 B 7 LEU A 284 ILE A 287 -1 N ILE A 285 O ILE A 302 SHEET 4 B 7 LEU A 256 ASP A 260 1 N ALA A 259 O LEU A 284 SHEET 5 B 7 ILE A 221 GLY A 226 1 N PHE A 224 O VAL A 258 SHEET 6 B 7 LYS A 145 ARG A 149 1 N ILE A 147 O ALA A 223 SHEET 7 B 7 VAL A 180 THR A 183 1 O LEU A 181 N SER A 148 SHEET 1 C 4 VAL A 374 ASP A 380 0 SHEET 2 C 4 LEU A 383 PHE A 388 -1 O GLU A 387 N GLU A 376 SHEET 3 C 4 ILE A 427 PHE A 430 -1 O LEU A 428 N VAL A 386 SHEET 4 C 4 ARG A 420 ALA A 421 -1 N ARG A 420 O GLY A 429 LINK C GLY A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N LEU A 2 1555 1555 1.34 LINK C HIS A 22 N MSE A 23 1555 1555 1.33 LINK C MSE A 23 N GLY A 24 1555 1555 1.34 LINK C ILE A 35 N MSE A 36 1555 1555 1.32 LINK C MSE A 36 N ALA A 37 1555 1555 1.33 LINK C LYS A 101 N MSE A 102 1555 1555 1.33 LINK C MSE A 102 N ILE A 103 1555 1555 1.32 LINK C GLY A 110 N MSE A 111 1555 1555 1.32 LINK C MSE A 111 N SER A 112 1555 1555 1.34 LINK C VAL A 158 N MSE A 159 1555 1555 1.34 LINK C MSE A 159 N THR A 160 1555 1555 1.32 LINK C SER A 195 N MSE A 196 1555 1555 1.34 LINK C MSE A 196 N SER A 197 1555 1555 1.32 LINK C GLU A 211 N MSE A 212 1555 1555 1.33 LINK C MSE A 212 N ILE A 213 1555 1555 1.33 LINK C THR A 271 N MSE A 272 1555 1555 1.32 LINK C MSE A 272 N PHE A 273 1555 1555 1.34 LINK C ALA A 288 N ALLP A 289 1555 1555 1.33 LINK C ALLP A 289 N GLY A 290 1555 1555 1.33 LINK C GLU A 346 N MSE A 347 1555 1555 1.33 LINK C MSE A 347 N ASP A 348 1555 1555 1.34 LINK C GLY A 381 N MSE A 382 1555 1555 1.34 LINK C MSE A 382 N LEU A 383 1555 1555 1.33 LINK C ALA A 421 N MSE A 422 1555 1555 1.32 LINK C MSE A 422 N PRO A 423 1555 1555 1.35 CISPEP 1 LEU A 175 PRO A 176 0 2.73 CISPEP 2 ALA A 178 PRO A 179 0 5.44 SITE 1 AC1 16 SER A 119 GLY A 120 SER A 121 TYR A 153 SITE 2 AC1 16 HIS A 154 GLY A 155 GLU A 227 ASP A 260 SITE 3 AC1 16 VAL A 262 VAL A 263 LLP A 289 THR A 326 SITE 4 AC1 16 HOH A 465 HOH A 491 HOH A 513 HOH A 530 SITE 1 AC2 4 LYS A 101 GLU A 244 LYS A 245 HOH A 485 SITE 1 AC3 6 LYS A 109 GLY A 110 ASP A 305 HOH A 509 SITE 2 AC3 6 HOH A 702 HOH A 774 CRYST1 113.224 59.577 85.337 90.00 130.59 90.00 C 1 2 1 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 0.008832 0.000000 0.007567 0.00000 SCALE2 0.000000 0.016785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015431 0.00000 MASTER 383 0 16 19 15 0 7 6 0 0 0 36 END