HEADER IMMUNE SYSTEM/CHOLINE BINDING PROTEIN 04-APR-13 4K12 TITLE STRUCTURAL BASIS FOR HOST SPECIFICITY OF FACTOR H BINDING BY TITLE 2 STREPTOCOCCUS PNEUMONIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT FACTOR H; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SUSHI DOMAIN (UNP RESIDUES 508-567); COMPND 5 SYNONYM: FACTOR H PROTEIN, H FACTOR 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CHOLINE BINDING PROTEIN A; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 68-148; COMPND 11 SYNONYM: CBPA; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CFH, HF, HF1, HF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 10 ORGANISM_TAXID: 1313; SOURCE 11 GENE: SPAR136_2333; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-PROTEIN COMPLEX, COMPLEMENT-BINDING COMPLEX, IMMUNE SYSTEM- KEYWDS 2 CHOLINE BINDING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.LIU,D.ACHILA,R.BANERJEE,E.MARTINEZ-HACKERT,Y.LI,H.YAN REVDAT 4 15-NOV-17 4K12 1 REMARK REVDAT 3 21-JAN-15 4K12 1 JRNL REVDAT 2 05-NOV-14 4K12 1 JRNL REVDAT 1 09-APR-14 4K12 0 JRNL AUTH D.ACHILA,A.LIU,R.BANERJEE,Y.LI,E.MARTINEZ-HACKERT,J.R.ZHANG, JRNL AUTH 2 H.YAN JRNL TITL STRUCTURAL DETERMINANTS OF HOST SPECIFICITY OF COMPLEMENT JRNL TITL 2 FACTOR H RECRUITMENT BY STREPTOCOCCUS PNEUMONIAE. JRNL REF BIOCHEM.J. V. 465 325 2015 JRNL REFN ISSN 0264-6021 JRNL PMID 25330773 JRNL DOI 10.1042/BJ20141069 REMARK 2 REMARK 2 RESOLUTION. 1.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 63060 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 3201 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.9671 - 3.0663 0.94 2636 131 0.1956 0.2098 REMARK 3 2 3.0663 - 2.4352 1.00 2690 151 0.1717 0.1956 REMARK 3 3 2.4352 - 2.1278 1.00 2664 137 0.1557 0.1635 REMARK 3 4 2.1278 - 1.9334 1.00 2655 125 0.1468 0.1693 REMARK 3 5 1.9334 - 1.7949 1.00 2665 115 0.1451 0.1537 REMARK 3 6 1.7949 - 1.6892 1.00 2598 140 0.1348 0.1464 REMARK 3 7 1.6892 - 1.6046 1.00 2625 146 0.1240 0.1467 REMARK 3 8 1.6046 - 1.5348 1.00 2597 158 0.1177 0.1307 REMARK 3 9 1.5348 - 1.4757 1.00 2640 121 0.1143 0.1239 REMARK 3 10 1.4757 - 1.4248 1.00 2581 160 0.1147 0.1421 REMARK 3 11 1.4248 - 1.3803 1.00 2567 154 0.1240 0.1477 REMARK 3 12 1.3803 - 1.3408 1.00 2597 151 0.1227 0.1283 REMARK 3 13 1.3408 - 1.3055 1.00 2580 144 0.1219 0.1228 REMARK 3 14 1.3055 - 1.2737 1.00 2618 128 0.1276 0.1634 REMARK 3 15 1.2737 - 1.2447 1.00 2594 145 0.1277 0.1513 REMARK 3 16 1.2447 - 1.2183 1.00 2563 139 0.1255 0.1266 REMARK 3 17 1.2183 - 1.1939 1.00 2584 138 0.1329 0.1714 REMARK 3 18 1.1939 - 1.1714 1.00 2572 149 0.1355 0.1574 REMARK 3 19 1.1714 - 1.1504 1.00 2572 131 0.1426 0.1734 REMARK 3 20 1.1504 - 1.1310 1.00 2598 123 0.1664 0.1652 REMARK 3 21 1.1310 - 1.1127 1.00 2575 141 0.1804 0.1852 REMARK 3 22 1.1127 - 1.0956 1.00 2547 149 0.2303 0.2811 REMARK 3 23 1.0956 - 1.0790 0.97 2541 125 0.2743 0.3075 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 55.28 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.91730 REMARK 3 B22 (A**2) : -1.57490 REMARK 3 B33 (A**2) : 2.49220 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 1268 REMARK 3 ANGLE : 1.243 1733 REMARK 3 CHIRALITY : 0.088 195 REMARK 3 PLANARITY : 0.006 224 REMARK 3 DIHEDRAL : 9.305 505 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4K12 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078756. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-12; 14-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.6; 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 21-ID-G; 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856; 1.45868 REMARK 200 MONOCHROMATOR : DIAMOND(111); KOHZU SI(111) REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD; MARMOSAIC REMARK 200 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63150 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.079 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.35900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3500, 0.1 M SODIUM ACETATE, PH REMARK 280 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. 20% REMARK 280 PEG3500, 0.1 M SODIUM ACETATE, SOAKED IN 0.5 M SODIUM IODIDE, PH REMARK 280 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.79350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.69100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.49250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.69100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.79350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.49250 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 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: 1290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 GLY B -1 REMARK 465 HIS B 0 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 ARG A 63 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 7 CE NZ REMARK 470 ARG B 9 CD NE CZ NH1 NH2 REMARK 470 GLU B 11 CD OE1 OE2 REMARK 470 GLU B 81 CG CD OE1 OE2 REMARK 470 LYS B 82 CG 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 OE2 GLU A 37 NZ LYS B 29 1.85 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 ASN A 25 -6.27 77.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 4K12 A 4 63 UNP P08603 CFAH_HUMAN 508 567 DBREF 4K12 B 2 82 UNP G6W2B2 G6W2B2_STREE 68 148 SEQADV 4K12 GLY A 0 UNP P08603 EXPRESSION TAG SEQADV 4K12 SER A 1 UNP P08603 EXPRESSION TAG SEQADV 4K12 HIS A 2 UNP P08603 EXPRESSION TAG SEQADV 4K12 MET A 3 UNP P08603 EXPRESSION TAG SEQADV 4K12 GLY B -1 UNP G6W2B2 EXPRESSION TAG SEQADV 4K12 HIS B 0 UNP G6W2B2 EXPRESSION TAG SEQADV 4K12 MET B 1 UNP G6W2B2 EXPRESSION TAG SEQADV 4K12 GLU B 61 UNP G6W2B2 GLN 127 CONFLICT SEQRES 1 A 64 GLY SER HIS MET SER CYS ASP ILE PRO VAL PHE MET ASN SEQRES 2 A 64 ALA ARG THR LYS ASN ASP PHE THR TRP PHE LYS LEU ASN SEQRES 3 A 64 ASP THR LEU ASP TYR GLU CYS HIS ASP GLY TYR GLU SER SEQRES 4 A 64 ASN THR GLY SER THR THR GLY SER ILE VAL CYS GLY TYR SEQRES 5 A 64 ASN GLY TRP SER ASP LEU PRO ILE CYS TYR GLU ARG SEQRES 1 B 84 GLY HIS MET ASP SER GLU ARG ASP LYS ALA ARG LYS GLU SEQRES 2 B 84 VAL GLU GLU TYR VAL LYS LYS ILE VAL GLY GLU SER TYR SEQRES 3 B 84 ALA LYS SER THR LYS LYS ARG HIS THR ILE THR VAL ALA SEQRES 4 B 84 LEU VAL ASN GLU LEU ASN ASN ILE LYS ASN GLU TYR LEU SEQRES 5 B 84 ASN LYS ILE VAL GLU SER THR SER GLU SER GLU LEU GLN SEQRES 6 B 84 ILE LEU MET MET GLU SER ARG SER LYS VAL ASP GLU ALA SEQRES 7 B 84 VAL SER LYS PHE GLU LYS FORMUL 3 HOH *255(H2 O) HELIX 1 1 GLY A 0 HIS A 2 5 3 HELIX 2 2 ASP B 2 SER B 27 1 26 HELIX 3 3 ARG B 31 GLU B 55 1 25 HELIX 4 4 SER B 58 LYS B 79 1 22 SHEET 1 A 2 SER A 4 ASP A 6 0 SHEET 2 A 2 TRP A 21 LYS A 23 -1 O PHE A 22 N CYS A 5 SHEET 1 B 4 ALA A 13 ARG A 14 0 SHEET 2 B 4 THR A 27 CYS A 32 -1 O GLU A 31 N ARG A 14 SHEET 3 B 4 THR A 44 GLY A 50 -1 O ILE A 47 N LEU A 28 SHEET 4 B 4 GLY A 53 TRP A 54 -1 O GLY A 53 N GLY A 50 SHEET 1 C 2 TYR A 36 GLU A 37 0 SHEET 2 C 2 TYR A 61 GLU A 62 -1 O TYR A 61 N GLU A 37 SSBOND 1 CYS A 5 CYS A 49 1555 1555 2.05 SSBOND 2 CYS A 32 CYS A 60 1555 1555 2.07 CRYST1 41.587 48.985 71.382 90.00 90.00 90.00 P 21 21 21 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 0.024046 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020414 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014009 0.00000