HEADER NUCLEOTIDE BINDING PROTEIN 30-MAR-10 3MDP TITLE CRYSTAL STRUCTURE OF A PUTATIVE CYCLIC NUCLEOTIDE-BINDING PROTEIN TITLE 2 (GMET_1532) FROM GEOBACTER METALLIREDUCENS GS-15 AT 1.90 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC NUCLEOTIDE-BINDING DOMAIN (CNMP-BD) PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER METALLIREDUCENS; SOURCE 3 ORGANISM_TAXID: 269799; SOURCE 4 STRAIN: GS-15 / ATCC 53774 / DSM 7210; SOURCE 5 GENE: GMET_1532; 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 STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, CYCLIC NUCLEOTIDE-BINDING KEYWDS 3 DOMAIN, DOUBLE-STRANDED BETA-HELIX FOLD, NUCLEOTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 17-JUL-19 3MDP 1 REMARK LINK REVDAT 3 08-NOV-17 3MDP 1 REMARK REVDAT 2 13-JUL-11 3MDP 1 VERSN REVDAT 1 19-MAY-10 3MDP 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE CYCLIC NUCLEOTIDE-BINDING JRNL TITL 2 PROTEIN (GMET_1532) FROM GEOBACTER METALLIREDUCENS GS-15 AT JRNL TITL 3 1.90 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13563 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 668 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 924 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1005 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 25.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.09000 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): 0.136 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.135 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.211 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1101 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 742 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1497 ; 1.511 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1815 ; 0.899 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 145 ; 7.160 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 43 ;31.624 ;23.023 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 189 ;13.983 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;16.884 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 176 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1251 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 226 ; 0.002 ; 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): 704 ; 1.760 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 281 ; 0.450 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1143 ; 2.931 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 397 ; 3.690 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 354 ; 5.445 ; 8.000 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 : 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 1 A 62 REMARK 3 ORIGIN FOR THE GROUP (A): 57.7594 19.3077 8.5474 REMARK 3 T TENSOR REMARK 3 T11: 0.0828 T22: 0.0406 REMARK 3 T33: 0.0345 T12: -0.0286 REMARK 3 T13: -0.0365 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 2.3998 L22: 2.4210 REMARK 3 L33: 1.5043 L12: 0.5974 REMARK 3 L13: -0.1004 L23: -0.3682 REMARK 3 S TENSOR REMARK 3 S11: 0.0249 S12: 0.0813 S13: -0.0673 REMARK 3 S21: -0.2394 S22: -0.0631 S23: 0.0169 REMARK 3 S31: 0.0677 S32: 0.0659 S33: 0.0382 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 72 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 60.9139 22.0603 14.3179 REMARK 3 T TENSOR REMARK 3 T11: 0.0607 T22: 0.0346 REMARK 3 T33: 0.0176 T12: -0.0241 REMARK 3 T13: -0.0247 T23: 0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.7788 L22: 1.9316 REMARK 3 L33: 1.2359 L12: 1.0602 REMARK 3 L13: 0.3171 L23: 0.4388 REMARK 3 S TENSOR REMARK 3 S11: 0.0899 S12: -0.0658 S13: 0.0192 REMARK 3 S21: 0.0391 S22: -0.0440 S23: -0.0671 REMARK 3 S31: 0.0841 S32: 0.0494 S33: -0.0459 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. ONE REMARK 3 SUCCINIC ACID (SIN) WAS MODELED IN THE PUTATIVE ACTIVE SITE REMARK 3 BASED ON THE PRESENCE OF CLEAR AND CONCLUSIVE ELECTRON DENSITY. REMARK 3 5. ONE ETHYLENE GLYCOL (EDO) MOLECULE FROM CRYSTALLIZATION IS REMARK 3 MODELED INTO THE STRUCTURE. REMARK 4 REMARK 4 3MDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058417. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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) : 0.91162,0.97922,0.97898 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR 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 : 13586 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 28.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.81400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10.0000% PEG-6000, 0.1M BICINE PH 9.0, REMARK 280 NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 47.93100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.93100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.93100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.93100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.93100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.93100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.93100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.93100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 0.000000 -1.000000 0.000000 95.86200 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 95.86200 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 35.48500 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 GLY A 0 REMARK 465 ASN A 63 REMARK 465 GLY A 64 REMARK 465 GLY A 65 REMARK 465 ALA A 66 REMARK 465 GLY A 67 REMARK 465 SER A 68 REMARK 465 ALA A 69 REMARK 465 ALA A 70 REMARK 465 ASN A 71 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 MSE A 1 CG SE CE REMARK 470 SER A 3 OG REMARK 470 LYS A 22 CG CD CE NZ REMARK 470 SER A 72 OG REMARK 470 GLU A 119 CD OE1 OE2 REMARK 470 GLN A 126 CD OE1 NE2 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 CYS A 75 CB CYS A 75 SG -0.116 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 PRO A 4 C - N - CA ANGL. DEV. = 21.4 DEGREES REMARK 500 PRO A 4 C - N - CD ANGL. DEV. = -20.2 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 SER A 3 70.02 -114.30 REMARK 500 ASN A 43 -7.14 80.60 REMARK 500 CYS A 75 143.54 -171.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 3 PRO A 4 -148.91 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 SIN A 142 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 143 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 402929 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3MDP A 1 141 UNP Q39VF8 Q39VF8_GEOMG 1 141 SEQADV 3MDP GLY A 0 UNP Q39VF8 LEADER SEQUENCE SEQRES 1 A 142 GLY MSE ILE SER PRO GLU ARG LEU ARG VAL TYR ARG PHE SEQRES 2 A 142 PHE ALA SER LEU THR ASP GLU GLN LEU LYS ASP ILE ALA SEQRES 3 A 142 LEU ILE SER GLU GLU LYS SER PHE PRO THR GLY SER VAL SEQRES 4 A 142 ILE PHE LYS GLU ASN SER LYS ALA ASP ASN LEU MSE LEU SEQRES 5 A 142 LEU LEU GLU GLY GLY VAL GLU LEU PHE TYR SER ASN GLY SEQRES 6 A 142 GLY ALA GLY SER ALA ALA ASN SER THR VAL CYS SER VAL SEQRES 7 A 142 VAL PRO GLY ALA ILE PHE GLY VAL SER SER LEU ILE LYS SEQRES 8 A 142 PRO TYR HIS TYR THR SER SER ALA ARG ALA THR LYS PRO SEQRES 9 A 142 VAL ARG VAL VAL ASP ILE ASN GLY ALA ARG LEU ARG GLU SEQRES 10 A 142 MSE SER GLU ASN ASN GLN ALA LEU GLY GLN VAL LEU MSE SEQRES 11 A 142 ASN ASN VAL ALA ALA ALA VAL LEU ALA ARG LEU HIS MODRES 3MDP MSE A 1 MET SELENOMETHIONINE MODRES 3MDP MSE A 50 MET SELENOMETHIONINE MODRES 3MDP MSE A 117 MET SELENOMETHIONINE MODRES 3MDP MSE A 129 MET SELENOMETHIONINE HET MSE A 1 5 HET MSE A 50 16 HET MSE A 117 8 HET MSE A 129 8 HET SIN A 142 8 HET EDO A 143 4 HETNAM MSE SELENOMETHIONINE HETNAM SIN SUCCINIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 SIN C4 H6 O4 FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *127(H2 O) HELIX 1 1 GLU A 5 VAL A 9 5 5 HELIX 2 2 TYR A 10 SER A 15 1 6 HELIX 3 3 THR A 17 ILE A 27 1 11 HELIX 4 4 GLY A 84 LEU A 88 5 5 HELIX 5 5 GLY A 111 ASN A 121 1 11 HELIX 6 6 ASN A 121 ARG A 139 1 19 SHEET 1 A 4 SER A 28 PHE A 33 0 SHEET 2 A 4 VAL A 104 ASN A 110 -1 O ASP A 108 N GLU A 29 SHEET 3 A 4 ASN A 48 GLU A 54 -1 N LEU A 49 O ILE A 109 SHEET 4 A 4 ILE A 82 PHE A 83 -1 O PHE A 83 N MSE A 50 SHEET 1 B 4 VAL A 38 PHE A 40 0 SHEET 2 B 4 SER A 97 ALA A 100 -1 O ALA A 98 N PHE A 40 SHEET 3 B 4 VAL A 57 PHE A 60 -1 N PHE A 60 O SER A 97 SHEET 4 B 4 THR A 73 VAL A 77 -1 O VAL A 74 N LEU A 59 LINK C MSE A 1 N ILE A 2 1555 1555 1.34 LINK C LEU A 49 N AMSE A 50 1555 1555 1.32 LINK C LEU A 49 N BMSE A 50 1555 1555 1.34 LINK C AMSE A 50 N LEU A 51 1555 1555 1.32 LINK C BMSE A 50 N LEU A 51 1555 1555 1.34 LINK C GLU A 116 N MSE A 117 1555 1555 1.33 LINK C MSE A 117 N SER A 118 1555 1555 1.33 LINK C LEU A 128 N MSE A 129 1555 1555 1.32 LINK C MSE A 129 N ASN A 130 1555 1555 1.33 CISPEP 1 LYS A 90 PRO A 91 0 5.39 SITE 1 AC1 11 PHE A 40 LEU A 59 PHE A 83 GLY A 84 SITE 2 AC1 11 VAL A 85 SER A 86 THR A 95 SER A 96 SITE 3 AC1 11 LEU A 137 ARG A 139 HOH A 161 SITE 1 AC2 8 ILE A 27 SER A 28 GLU A 29 LYS A 31 SITE 2 AC2 8 ASN A 48 ASP A 108 ASN A 110 HOH A 199 CRYST1 95.862 95.862 35.485 90.00 90.00 90.00 P 4 21 2 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 0.010432 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010432 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028181 0.00000 MASTER 420 0 6 6 8 0 5 6 0 0 0 11 END